The Pakistan Army does not merely tolerate terrorism. It manages terrorism. The distinction is not rhetorical, and it is not a matter of degree. It is the central analytical claim that any honest reckoning with the Indian subcontinent’s longest unfinished conflict must eventually confront. Tolerance suggests passivity, an institution that looks the other way while bad actors do bad things. Management suggests something else: an institution that selects which groups receive training, which leaders receive protection, which attacks receive authorization, which front organizations receive legitimacy, and which clients are quietly dropped when their utility expires. Tolerance is what Pakistan’s diplomats describe when they speak abroad. Management is what the historical record describes when it is read carefully.

This article is the analytical foundation for understanding why Pakistan’s terror infrastructure has survived four decades of international pressure, why it has produced the deadliest non-state attacks of the last quarter century, and why the covert campaign now systematically dismantling its leadership operates with the efficiency of an institution penetrating a familiar bureaucracy rather than an enemy unknown. The shadow war is not targeting terrorists in a vacuum. It is targeting the Pakistan Army’s clients, and every successful elimination is a demonstration that the Army cannot protect what it created. To grasp why the campaign reaches the people it reaches, in the cities it reaches them in, with the precision it brings to the work, the reader must first understand what the campaign is actually fighting against. It is fighting against an institutional relationship, not a movement. It is fighting against the patronage networks of a uniformed bureaucracy that has, since the late 1970s, treated militant violence as one tool among many in the management of national strategy.

The relationship is not uniform. The Army does not relate to every terror group the same way. Lashkar-e-Taiba is treated differently from Jaish-e-Mohammed, which is treated differently from Hizbul Mujahideen, which is treated very differently from the Tehreek-e-Taliban Pakistan that has been killing Pakistani soldiers in significant numbers for over a decade. The Khalistan groups, which the Army uses to needle India in the diaspora, occupy a different category still. What follows is a structural analysis of these differential relationships, the historical conditions that produced them, the doctrinal logic that sustains them, the operational mechanics that make them work, and the question that defines the contemporary debate: has the Army lost control of the groups it created, or does it retain sufficient direction to activate and deactivate them as strategic needs change? The answer matters because it determines whether the safe haven can be dismantled by Pakistan if Pakistan ever decided to dismantle it, or whether the relationship has hardened into something that even the Army’s senior leadership cannot now reverse.

Origins of the Nexus: From Partition to the Afghan Jihad

The institutional relationship between Pakistan’s military and its militant proxies did not begin in the 1980s. It began at Partition. The 1947 tribal lashkar invasion of Kashmir, organized by Pakistani military officers but conducted by irregular fighters from the North-West Frontier, established a template that would persist for seventy-five years. The template held that Pakistan’s regular forces would not directly contest Indian Kashmir, because direct contestation would invite full-scale war that Pakistan could not win, but irregular forces would do the work the regular forces could not, and the state would maintain plausible deniability about the relationship. The 1947 lashkar was not a terror group in the modern sense. It was a tribal levy commanded by serving and recently retired officers. But the doctrinal lesson, that violence by irregulars could be cheaper, more deniable, and ultimately more politically effective than violence by uniforms, was internalized at the founding.

The 1965 war reinforced the lesson in failure. Operation Gibraltar, the infiltration of Pakistani regular and irregular forces into Indian Kashmir to spark an uprising, failed catastrophically. The expected Kashmiri uprising did not materialize. Indian forces responded by crossing the international border. Pakistan was militarily defeated and politically embarrassed. But the institutional memory that the Pakistan Army drew from 1965 was not that proxy warfare did not work. It was that proxy warfare conducted by uniformed personnel posing as irregulars could be detected and counter-attacked, while proxy warfare conducted by genuine non-state actors could not. The next iteration, when it came, would use real civilians, real religious networks, and real ideological motivation, not commando regiments wearing local clothes.

That iteration came under General Muhammad Zia-ul-Haq, who seized power in 1977 and ruled until his death in a still-unexplained plane crash in August 1988. Zia’s eleven years in power were the formative period of the modern Pakistan Army-militant nexus. Three forces converged in his presidency. First, Zia personally was a devout Deobandi Muslim who believed Pakistan should be reorganized around Islamic principles, and who saw militant Islamism as a strategic asset rather than a threat. Second, the Soviet invasion of Afghanistan in December 1979 created an external crisis that Pakistan, with American and Saudi backing, would manage through the largest covert program of the Cold War. Third, the Iranian Revolution earlier the same year had shifted the regional balance in ways that made Sunni militant networks attractive as instruments of statecraft, both against Soviet-backed Afghanistan and against the new Shia regime in Tehran.

The Inter-Services Intelligence directorate, which had existed since 1948 as a small body coordinating the three armed services, was transformed during the Afghan jihad into the operational arm of an enormous proxy war. Billions of dollars in American and Saudi funding flowed through ISI to seven Afghan mujahideen factions, with ISI selecting which factions received which weapons in which quantities. This was not assistance. It was operational direction. The selection criteria favored the most ideologically rigid and Pakistan-loyal factions, particularly Gulbuddin Hekmatyar’s Hezb-e-Islami, even when American and Afghan field commanders argued that other factions were more militarily effective. The American intelligence community accepted ISI’s primacy because no alternative existed. Pakistan was the supply route, the training infrastructure, the diplomatic shield. ISI ran the war.

What the Afghan jihad taught the Pakistan Army was that an entire generation of fighters could be produced through a network of madrassas, training camps, charitable organizations, and operational handlers, and that the resulting fighters could be deployed wherever the Army chose. The fighters did not need to know they were instruments of state policy. The madrassas could teach them genuine theological commitment. The training camps could give them genuine military skills. The charitable organizations could provide them genuine humanitarian cover. Their motivation could be authentic and their utility could still be calculated. The doctrinal innovation was the recognition that the most effective proxy was one who did not perceive itself as a proxy.

The Soviet withdrawal from Afghanistan in 1989 and the collapse of the Soviet Union in 1991 should have closed the proxy infrastructure. The proximate purpose for which it had been built no longer existed. American funding stopped almost immediately. Saudi funding declined. The Afghan factions began their civil war, which would eventually produce the Taliban and Al-Qaeda. The training camps in Pakistan-administered Kashmir and the Pakistani interior could have been dismantled. They were not. Within months of the Soviet withdrawal, the same infrastructure was being repurposed for the Kashmir insurgency that erupted in 1989, and which Pakistan’s military establishment would manage for the next three decades using techniques developed during the Afghan jihad.

The Kashmir redirection was not accidental. It was a conscious institutional decision. The Soviet collapse coincided with rising indigenous unrest in Indian-administered Kashmir, driven by domestic grievances that had little to do with Pakistan. The Pakistan Army, observing that unrest, decided that a Pakistan-supported insurgency offered a low-cost way to bleed India through Kashmir, building on what Zia had described in private memos as the doctrine of bleeding the Indian elephant by a thousand cuts. The infrastructure built for Afghanistan, the training camps, the safe houses, the recruitment networks, the funding channels, the protection mechanisms, was retained and redirected. The personnel who had run the Afghan operation became the personnel who ran the Kashmir operation. The Inter-Services Intelligence’s S-Wing, dedicated to the Kashmir campaign, drew its operational expertise directly from the Afghan war.

By the mid-1990s, the proxy infrastructure had produced its first generation of organizations specifically designed for the Kashmir operation. Hizb-ul-Mujahideen was founded in 1989 by Mohammad Ahsan Dar with explicit Pakistani support, and would soon become the largest Kashmir-focused militant group. Lashkar-e-Taiba was founded in 1986 by Hafiz Saeed and Zafar Iqbal as the militant wing of Markaz Dawa-wal-Irshad, a Salafist organization that had received Saudi and Pakistani funding during the Afghan jihad and which now turned its attention to Kashmir. Jaish-e-Mohammed would be founded later, in 2000, by Masood Azhar after his release in the IC-814 hijacking exchange. Each of these organizations was created with direct Pakistani military involvement. None of them existed independently of the patronage networks that produced them. None of them could have built their training infrastructure, recruitment apparatus, or operational capability without the institutional support that the Army provided.

The crucial question, which becomes urgent in the contemporary debate, is whether this origin story makes the organizations permanent instruments of the state, or whether it makes them now-autonomous actors who happen to share the state’s preferences. The institutional origins are clear. The institutional present is contested. The shadow war is the test that is forcing that question to the surface.

The institutional culture that grew up around the proxy infrastructure deserves separate attention. Within the Pakistan Army, certain commands and certain career paths became associated with the proxy operation. Officers who served on the Afghan border, in the Kashmir-facing formations, or in specific ISI directorates accumulated knowledge and relationships that became valuable institutional assets. Some of these officers rose to senior positions partly on the basis of their familiarity with the proxy networks. The internal incentive structure of the Army therefore came to reward expertise in managing militant relationships, not just expertise in conventional military skills. This had downstream effects on doctrine, on personnel selection, and on how the institution understood its own purpose. An Army that institutionalizes proxy management as a career-relevant skill is an Army whose senior leadership will inevitably include people whose professional identity is tied to maintaining the relationships. The cost of dismantling the relationships is therefore not only strategic but personal for significant numbers of senior officers. They would be dismantling their own careers, their own networks, and their own claim to institutional value. This personal-stakes dimension of the doctrine is rarely discussed in policy analyses but is essential to understanding why the doctrine persists despite costs that, in purely strategic terms, would seem to argue against its continuation.

The civilian-military relationship in Pakistan also shapes the doctrine’s persistence. Pakistan’s civilian governments have, at various points, attempted to shift policy on militant organizations. Benazir Bhutto’s government in the 1990s made gestures in this direction. Nawaz Sharif’s various governments did the same. Imran Khan’s government from 2018 to 2022 produced rhetoric about ending the doctrine. None of these civilian initiatives produced sustained change. The reason is that civilian institutions in Pakistan have limited operational influence over national security policy. The Army controls intelligence, foreign affairs in matters of strategic concern, and significant portions of the security apparatus. Civilian governments can announce policies. They cannot enforce policies that the Army does not support. The doctrine has persisted because civilian opposition to it, when it has existed, has not been able to translate into actual change. The Pakistani political system’s structure makes the doctrine resistant to electoral pressure in a way that few other policy domains are. This structural feature of Pakistani governance is itself a function of how the doctrine has been institutionalized over decades.

The Strategic Doctrine: Why the Establishment Chose Proxies

The choice was not inevitable. Other states facing similar strategic situations have made different choices. India, facing comparable security pressures from Pakistan, has historically declined to use militant proxies as instruments of state policy. Iran has used militant proxies but in different ways and for different purposes. The Pakistan Army’s specific reliance on Sunni militant networks as instruments of statecraft against India is the result of a particular strategic doctrine, articulated by particular thinkers, in response to particular structural conditions. Understanding why the doctrine emerged matters because it determines what would be required to replace it.

The doctrine has been variously called strategic depth, asymmetric warfare, low-intensity conflict, and bleeding by a thousand cuts. The phrasings differ but the underlying logic is consistent. Pakistan’s conventional military disadvantage relative to India is structural and permanent. India’s economy, population, and territory are all multiples of Pakistan’s. In any sustained conventional war, demographic and economic mass will matter more than any temporary advantage that doctrine, equipment, or alliance can produce. A conventional military strategy that relies on direct force-on-force engagement is therefore a strategy that Pakistan cannot win. The conclusion the establishment drew, beginning under Zia and articulated through subsequent army chiefs, was that conventional restraint must be paired with sub-conventional aggression. Pakistan would not start wars it could not win, but it would maintain a constant low-intensity pressure on India that India could not respond to without escalating to a war that would devastate both countries and risk nuclear use.

The nuclear acquisition completed the doctrinal frame. Pakistan’s nuclear weapons are not primarily intended to deter Indian invasion, although that is their stated purpose. They are primarily intended to deter Indian conventional escalation in response to Pakistani sub-conventional provocation. The structure works as follows. Pakistan supports militant attacks against India. India considers conventional retaliation. Pakistan signals that conventional retaliation could escalate to nuclear use. India declines to escalate. The militant attacks continue. The cycle has held since the 1990s. It is the operational logic that the proxy infrastructure exists to serve.

The doctrine has been articulated by named thinkers within the establishment. General Mirza Aslam Beg, army chief from 1988 to 1991, was an early proponent of strategic depth in Afghanistan, arguing that Pakistan’s defensive posture required a friendly Afghan government that could provide rear-area security. General Hamid Gul, ISI director from 1987 to 1989, extended the doctrine to militant proxies as instruments of regional influence, and continued to articulate it in retirement until his death in 2015. General Pervez Musharraf, army chief from 1998 to 2007 and president from 2001 to 2008, in his memoir In the Line of Fire, defended the use of militant networks against India as a legitimate response to Indian intransigence on Kashmir, while simultaneously arguing that he had cracked down on those same networks. The contradictions in Musharraf’s account reflect the doctrine’s internal tensions, but they do not undermine its existence. The doctrine has been the consistent operating logic of the Pakistani establishment since the late 1980s.

The international response to the doctrine has been ineffective for structural reasons. Pakistan’s geographic position made it indispensable during the Afghan jihad and again after September 11, 2001. American policy could not afford to push Pakistan past the point of cooperation. The Financial Action Task Force grey-listing and white-listing process has produced incremental changes in Pakistan’s approach to terror financing but has not altered the underlying doctrine. The United Nations Security Council sanctions on individuals and organizations have inconvenienced specific actors without dismantling the patronage system. International pressure has failed because no external actor has been willing to absorb the costs of pushing Pakistan to the point where the doctrine becomes untenable. The doctrine’s resilience is a function of the international system’s structure, not of the doctrine’s internal merits.

The post-September 11 period offered the clearest test of how the doctrine survives under maximum international pressure. After the attacks, the United States demanded Pakistani cooperation against Al-Qaeda and the Taliban. President Pervez Musharraf agreed to a public realignment, ended formal Pakistani support for the Afghan Taliban, and arrested several hundred Al-Qaeda figures including Khalid Sheikh Mohammed in Rawalpindi in March 2003. The cooperation was real and produced significant operational results for the American counter-terror effort. But the cooperation was also strictly bounded. The networks that supported the Afghan Taliban were not dismantled, only displaced. The Quetta Shura, where senior Taliban leadership relocated after their flight from Afghanistan, operated for years from a Pakistani city of nearly a million people without serious Pakistani action against it. The Haqqani network, which conducted some of the most lethal attacks against American forces in Afghanistan, retained its operational base in North Waziristan and its institutional protection from elements within the Pakistani establishment. Musharraf’s autobiography, In the Line of Fire, defends this selectivity by arguing that Pakistan made distinctions between terrorists who threatened Pakistan and those who served Pakistani strategic interests. The distinction itself was the doctrine. The American intelligence community recognized the pattern but could not act on it without breaking the cooperation that the rest of the post-September 11 strategy required.

The Mumbai attacks of November 2008 produced the second great test of international pressure on the doctrine. The attacks killed 166 people, including six Americans and several other foreign nationals. The operational planning was unambiguously located in Pakistan. The training facilities used by the attackers were in Pakistani territory. The handlers who directed the attackers in real time were on Pakistani phones. American, Indian, and British intelligence services produced detailed evidence of the LeT command-and-control structure that authorized and executed the operation. The pressure on Pakistan was enormous. Hafiz Saeed was placed under house arrest. Zaki-ur-Rehman Lakhvi was detained. Promises of trials and accountability were issued. Yet within years, Saeed had been released, Lakhvi had returned to operational direction from inside detention, and the LeT organizational infrastructure remained intact. The Pakistani judicial system found procedural reasons to release each major figure. The international pressure proved insufficient to overcome the institutional commitment to the doctrine. The Mumbai case became a textbook example of how the doctrine could absorb even the most damaging international scrutiny and continue functioning.

The Financial Action Task Force grey-listing process from 2018 to 2022 represented a different kind of pressure, focused on the financial architecture rather than the operational personnel. The grey-listing imposed real economic costs on Pakistan, particularly during a period of acute economic difficulty. The Pakistani government responded with legislative changes, prosecutions of mid-tier figures, and public commitments to dismantle terror financing networks. Some of these changes were substantive. Others were performative. The outcome was that Pakistan was eventually removed from the grey list in 2022, with the FATF concluding that sufficient progress had been made. The militant organizations whose financing was supposedly being targeted continued to function. The leadership remained in place. The infrastructure remained intact. The grey-listing process demonstrated that Pakistan could absorb significant economic pressure without altering the underlying doctrine, although the experience may have produced some learning about how to manage the financial mechanics more discreetly.

The American withdrawal from Afghanistan in August 2021 changed the international calculus in ways that have not yet fully played out. Without the Afghan operational requirement, American leverage on Pakistan diminished significantly. The strategic importance of the Pakistani relationship declined for the United States, even as Chinese influence in Pakistan grew. The reduced American pressure has allowed Pakistan to rebuild aspects of its proxy infrastructure that had been constrained during the Afghan campaign. But the reduced pressure has also reduced the international cover that allowed the doctrine to operate beneath the surface. The shadow war’s emergence in the post-2021 period is partly a function of this reduced international cover. As the United States withdrew its protective umbrella, the space for unilateral Indian counter-terror action expanded. The Pakistani establishment now finds itself maintaining the doctrine without the international protection that had previously allowed it to absorb consequences.

The Relationship Spectrum: Mapping Five Modes of Engagement

The Pakistan Army does not relate to every militant group in the same way. The relationship varies by organization, by period, by individual leadership, and by strategic context. Mapping the variation is necessary because generic claims about state sponsorship miss the most important analytical features of how the relationship actually works. What follows is a five-tier spectrum that captures the differential modes of engagement, with named organizations placed on the spectrum according to the available evidence. The spectrum runs from full operational control on one end to active hostility on the other, with three intermediate categories in between.

The first tier is full operational control. In this mode, the militant group functions as a direct extension of state intelligence and military planning. Operations are authorized at the state level. Targets are selected at the state level. Personnel are vetted at the state level. The militant organization exists as a deniable instrument of the state, and its leadership understands itself in those terms. The clearest examples in this tier are specific Jaish-e-Mohammed operations, particularly those that closely tracked Pakistani strategic interests at the moment of execution. The 2001 Indian Parliament attack, which produced the largest India-Pakistan crisis since 1971, occurred at a moment when the Musharraf government was navigating a complex post-September 11 environment, and the attack’s timing and targeting suggested either operational direction or operational acquiescence at very high levels. The 2016 Pathankot attack and the 2019 Pulwama attack, both attributed to JeM, occurred at moments when the Pakistani establishment had reasons to test Indian responses. Whether each individual operation was specifically authorized or merely permitted is the kind of question that sources within the establishment would need to answer, and they have not. But the cumulative pattern of JeM operations in moments of strategic significance is consistent with operational control rather than autonomous initiative.

The second tier is strategic direction with operational autonomy. In this mode, the militant group operates on broad strategic guidance from the establishment but conducts specific operations using its own planning and personnel. The state sets the parameters. The organization fills in the details. Lashkar-e-Taiba sits firmly in this tier. The 26/11 Mumbai attacks, in which ten LeT operatives killed 166 people across multiple Mumbai locations over three days in November 2008, represent the model. The intelligence consensus, including the testimony of David Coleman Headley to American investigators, is that the operation was planned by LeT operational leadership including Sajid Mir and Zaki-ur-Rehman Lakhvi. ISI personnel were in contact with the operational team during the attack. The Mumbai attack required strategic permission and operational coordination that LeT could not have produced without state acquiescence, but the specific tactical decisions were made by LeT commanders, not by uniformed officers. LeT’s training infrastructure at the Markaz-e-Taiba in Muridke, its fundraising through Jamaat-ud-Dawa, and its operational planning through its various wings, all proceed under what looks like strategic direction with significant operational autonomy. The complete analysis of LeT’s organizational architecture and its relationship to the establishment is the subject of the definitive guide to Lashkar-e-Taiba’s structure and operations, and the JeM organizational portrait examines how Masood Azhar’s organization developed its different relationship with state institutions.

The third tier is patronage and protection. In this mode, the establishment does not direct operations and may not closely manage the organization, but it provides essential protection that allows the leadership to function. Safe residences. Police non-interference. Travel facilitation. Documentary cover. Hizbul Mujahideen’s exile leadership in Pakistan-administered Kashmir and in Pakistan proper has historically operated in this mode. Syed Salahuddin, the Hizbul Mujahideen supreme commander based in Muzaffarabad, has held press conferences, given interviews to international media, and chaired meetings of the United Jihad Council, all from Pakistani territory, with no apparent concern about prosecution. He has not been arrested. He has not been deported. He has not faced charges. The protection is consistent and durable. But the operational direction appears to be more limited than in the case of LeT or specific JeM operations. Hizbul plans its own activities. The state simply ensures that those activities are not interrupted by Pakistani law enforcement.

The fourth tier is benign neglect. In this mode, the establishment is aware of the organization’s presence and activities, does not actively support them, but also does not interfere. The Khalistan separatist groups operating from Pakistani territory occupy this tier. Pakistan’s interest in the Khalistan groups is primarily diplomatic and tactical. They are useful when India needs to be irritated, particularly during diplomatic disputes. They are tolerated rather than directed. The Khalistan Commando Force leadership in Lahore, including Paramjit Singh Panjwar before his elimination in May 2023, lived in Pakistan with Pakistani-issued documents. The state did not run their operations, but it provided the territory in which they could exist. When Panjwar was killed by unknown gunmen in Lahore, Pakistani authorities issued the standard pro forma investigation announcements without genuine pursuit. The pattern suggested protection that was real but not robust, presence that was tolerated but not directed.

The fifth tier is adversarial. The Tehreek-e-Taliban Pakistan, which has killed thousands of Pakistani soldiers and civilians in attacks across Khyber Pakhtunkhwa and other regions since its emergence in 2007, is the example. The establishment’s relationship with TTP is the opposite of the relationship with LeT or JeM. The Army has conducted multiple major military operations against TTP, including Operation Rah-e-Rast in Swat in 2009 and Operation Zarb-e-Azb in North Waziristan from 2014. Senior TTP leaders have been killed in Pakistani operations or in American drone strikes that the Pakistani government did not actively obstruct. The relationship is not patronage. It is suppression. But the suppression is uneven. Elements within TTP’s predecessor networks were once patronized by the establishment during the Afghan jihad, and the institutional knowledge that connects the Army to TTP’s social and ideological roots has not been used to prevent TTP from existing, only to push back against TTP’s specific anti-state operations.

The spectrum reveals what a unified state-sponsorship narrative obscures. The Pakistan Army is not a single actor with a single relationship to terrorism. It is an institution with differentiated relationships to different organizations, and those relationships shift over time. LeT has historically been a strategic asset against India, more reliable and more capable than other groups, and the establishment has invested in its long-term sustainability. JeM has been a more violent and less controllable instrument, useful for specific operations but harder to manage. Hizbul has been a Kashmir-focused tool that does not require ongoing direction, only protection. The Khalistan groups have been a low-cost diplomatic irritant. TTP has been a domestic threat that must be suppressed. The institutional response to each has been calibrated to its strategic role.

The differentiation matters operationally because it determines what kind of pressure works on which group. International sanctions on LeT have produced superficial compliance and substantive continuity. Military operations against TTP have produced real degradation. Diplomatic pressure on Khalistan groups has produced occasional gestures and limited substance. The shadow war’s selectivity in target selection, focusing on LeT, JeM, Hizbul, and Khalistan operatives while ignoring TTP, reflects an analytic understanding that the campaign is targeting state-sponsored networks rather than terrorism in general. The targets are chosen because they are India’s enemies, and they are India’s enemies because the establishment has chosen to make them so. The infrastructure that protects them, the safe haven network across Pakistani cities, is the operational expression of the relationship spectrum. Where the Army’s relationship is closer, the protection is more robust. Where the relationship is looser, the protection is thinner. The shadow war’s progress through the spectrum is itself diagnostic.

The spectrum has also shifted over time in ways that the contemporary snapshot does not capture. In the late 1980s and early 1990s, the establishment’s relationship with multiple Kashmiri groups was direct and operationally close. The Hizb-ul-Mujahideen of that period received substantial direct support and operational direction. As the Kashmir insurgency matured and as international scrutiny intensified, the relationship evolved. By the 2000s, the establishment had pulled back from direct operational direction of most Kashmiri groups while maintaining the protection and infrastructure functions. LeT’s rise during this period reflected its capacity to operate with greater discipline and less visible state direction, which made it more useful in the post-September 11 environment. JeM filled a different niche, conducting more spectacular and more politically risky operations. The current relationship structure is the accumulated result of these adaptations, not a static template that has remained unchanged for decades.

A further complication is the role of retired officers in maintaining the relationships. The institutional infrastructure depends not only on serving personnel but on retired officers who continue to provide guidance, legitimacy, and connections. Several prominent retired Pakistani generals have publicly defended militant organizations, served on advisory boards of charitable fronts, or maintained personal relationships with militant leaders. Lieutenant General Hamid Gul, after his retirement as ISI director in 1989, became one of the most visible public defenders of the militant networks, giving interviews and writing columns that articulated the doctrine in unusually candid terms. He died in 2015, but the role he played has been replicated by others. The retired-officer community provides an institutional bridge between past and present, ensuring that personnel changes at senior levels do not disrupt the continuity of the relationship. The retired officers carry the institutional memory that newer officers may not yet have absorbed. They carry the personal relationships that institutional protocols cannot create. They carry the political cover that allows serving officers to maintain relationships without taking direct public responsibility for them.

How the Management Works: Training, Protection, Authorization, Legitimization

If the spectrum describes the modes of engagement, the management mechanics describe how each mode functions in practice. The Army-militant relationship is sustained through four operational levers: training, protection, authorization, and legitimization. Each lever has institutional infrastructure behind it. Each can be observed in specific cases and traced through specific personnel. The combination of all four is what distinguishes a managed relationship from a tolerated one.

Training is the first lever. The training infrastructure for India-focused militant groups operates in two geographic concentrations. The first is in Pakistan-administered Kashmir, in facilities near the Line of Control that allow rapid infiltration into Indian Kashmir. The second is in the Pakistani heartland, particularly in Punjab, where the larger and more established camps are protected by their distance from the international border and by the surrounding Pakistani population. The Markaz-e-Taiba complex in Muridke, on two hundred acres outside Lahore, is the most documented example, but it is not unique. JeM’s complex in Bahawalpur serves a similar function for that organization. Smaller training facilities operate in rural areas across Punjab and parts of Sindh, often co-located with madrassas that provide religious instruction and ideological framing alongside the military skills.

The training itself draws on Pakistani military expertise. Former Special Services Group operators, retired infantry officers, and serving personnel detailed to ISI’s S-Wing have all reportedly contributed to militant training over the years. The skills taught include small arms, explosives, urban tactics, infiltration, communications discipline, and counter-surveillance. The 26/11 attackers demonstrated capabilities that required this kind of training, including their use of GPS for coastal navigation, their satellite phone communications, and their tactical coordination during the three-day siege. None of these capabilities could have been developed through autodidactic learning in a madrassa. They required instructors with relevant operational experience, equipment with relevant specifications, and time for genuine skill acquisition. The training infrastructure that produced the 26/11 attackers has been documented in Indian, American, and international intelligence assessments. It has not been dismantled.

The training pipeline integrates several distinct phases. Initial recruitment occurs through religious networks, particularly through the network of Deobandi madrassas in southern Punjab and parts of KPK province that have historically supplied volunteers for both Afghan and Kashmir operations. Recruitment is supplemented by direct outreach in particular districts where economic conditions, family traditions of military service, or specific local grievances produce reliable candidates. Initial ideological training takes place in the religious institutions or in dedicated indoctrination facilities. Basic military training follows, often in the smaller camps that focus on weapons handling and physical conditioning. Advanced training is reserved for vetted candidates who have demonstrated reliability and who are being prepared for specific operational roles. The graduates of advanced training become operational personnel for major attacks or trainers for the next generation of recruits. The pipeline is not separate from Pakistani military training infrastructure. It overlaps with it, draws on it, and depends on it. The institutional knowledge that allows the pipeline to function is the same institutional knowledge that produces Pakistani military officers.

Protection is the second lever. The protection mechanism operates through three layers. The first layer is the prevention of arrest. Senior militant leaders live openly in Pakistani cities under their own names or thinly veiled aliases. They travel within Pakistan without being intercepted. They hold meetings, give speeches, and conduct organizational business. The Pakistani police, intelligence services, and prosecutorial authorities do not pursue them. When international pressure produces a public arrest, the arrest is typically followed by either a quick release on bail, a prosecution that fails on procedural grounds, or a detention that is converted into protective custody allowing operational continuity. Hafiz Saeed has been arrested multiple times since 26/11. He has also been released multiple times. Zaki-ur-Rehman Lakhvi was held for years in conditions that allowed him to direct LeT operations from inside detention, including the alleged fathering of a child while supposedly in custody. The pattern is not accidental. It is institutional.

The second protection layer is the prevention of foreign access. International investigators seeking to interview Pakistani-resident militants face systematic obstruction. Indian requests for extradition are denied. American FBI requests for access to specific individuals during active investigations have been refused or delayed past the point of operational utility. The 26/11 investigation, which involved extensive American cooperation given the presence of American victims, did not produce access to senior LeT leadership in any form that could support prosecution. The protection extends to documentary records: phone intercepts, financial records, and communications that would establish operational links between militants and state personnel are not made available to foreign investigators. The protection is not passive. It is an active institutional function performed by Pakistani intelligence, the Foreign Office, and the legal system in coordination.

The third protection layer is physical security. Senior militant leaders receive security details that are often staffed by serving or retired military and police personnel. Their residences are located in neighborhoods with physical security infrastructure. Their movements are coordinated with local authorities to ensure protection during travel. The shadow war’s eliminations have repeatedly demonstrated that this physical protection is real but penetrable. Sardar Hussain Arain, the JuD figure killed in Sindh, had local protection that did not stop the operation. Bashir Ahmad Peer, the Hizbul exile leader killed in Rawalpindi, lived in a city where the Pakistani military’s presence is denser than anywhere else in the country, and his elimination occurred there nonetheless. The shadow war is, among other things, a stress test of the physical protection layer, and the campaign’s continued progress demonstrates that the layer has gaps. The complete analysis of the Hizbul commander killed in Rawalpindi examines this case in detail.

Authorization is the third lever. The authorization function is the most sensitive, because it goes to the question of state responsibility for specific attacks. The strongest claim, that specific senior officers personally authorized specific attacks, requires evidence that intelligence services rarely produce. The weaker claim, that the institutional culture of the establishment permitted attacks that the establishment could have prevented, is supported by the historical record but is harder to attach to specific personnel. What is documented is that major attacks attributed to LeT and JeM occurred at moments when their occurrence served broader Pakistani strategic interests, that the operational planning required infrastructure only available with state acquiescence, and that no major attack produced internal accountability within the militant organization or against specific Pakistani officers. The absence of consequences is itself evidence of authorization at the institutional level.

Legitimization is the fourth lever. The legitimization function operates through the construction of front organizations that present militant groups as charitable, religious, or political entities deserving of public legitimacy and international engagement. Jamaat-ud-Dawa, the front organization for LeT, has functioned for years as an ostensibly charitable entity providing disaster relief, education, and healthcare. Its earthquake response in 2005 was widely praised in Pakistani public discourse. Its educational network reaches hundreds of thousands of students. Its medical facilities serve real patients. The dual-use structure is not coincidental. It is the operational design. The charitable activities are real. The militant activities are also real. The same organization, the same personnel, the same financial flows, the same physical infrastructure, support both functions. The legitimization function makes this possible by creating the public-facing identity that allows the group to operate openly even after international designation.

The legitimization function extends into the Pakistani political system. The Milli Muslim League, founded as the political wing of JuD, contested elections in 2018 before being denied registration. Hafiz Saeed’s son ran for parliament. Allied religious parties have provided ideological cover and political support. The militant organizations have sought political legitimacy not because they need votes but because parliamentary presence offers protection from prosecution and constraints on state action against them. The establishment has alternately permitted and constrained these political ventures, never decisively shutting them down. The pattern is consistent with management rather than acquiescence.

The four levers operate together. Training without protection produces capable fighters who get arrested before they can be deployed. Protection without authorization produces sheltered figures whose attacks are not directed by anyone. Authorization without legitimization produces operations whose state attribution becomes politically untenable. Legitimization without training produces public identities without operational capacity. The integration of all four is what distinguishes the Pakistan Army’s relationship with militant groups from less developed forms of state-militant interaction elsewhere in the world. The integration is institutional, not personal. It does not depend on which general happens to be in command at a given moment. It is the system that produces the personnel, not the personnel that produce the system. The intelligence apparatus that manages these relationships at the operational level is the subject of dedicated analysis, but the apparatus exists within and serves the institutional preferences of the broader establishment.

A fifth lever, less often discussed but no less important, is the financial architecture that sustains the militant infrastructure. The financial system operates through multiple overlapping channels. Charitable donations, often raised through the front organizations during religious festivals and disaster-relief appeals, provide a public-facing income stream that can be presented to international scrutiny as legitimate civil-society activity. Hawala transfers move funds across borders without leaving the kind of trail that formal banking systems produce, allowing money to enter Pakistan from Gulf states and from the Pakistani diaspora without creating documentary evidence of its origin or destination. Real-estate holdings, both inside Pakistan and abroad, function as both an investment vehicle and a money-laundering mechanism. Commercial businesses owned by leadership figures or front organizations generate revenue that can be commingled with militant operations. Direct state subsidies, whether routed through ISI budgets or through other less visible channels, supplement the publicly accountable income streams. The financial architecture has been studied extensively by international financial intelligence agencies, and the FATF process forced specific reforms in some of its components, but the underlying structure has proven resilient to disruption.

The recruitment pipeline draws on social conditions that the establishment did not create but that it has chosen not to disrupt. Specific districts in Pakistan have produced disproportionate numbers of militants over decades. The reasons are mixed. Economic conditions in those districts are often poor, providing a pool of young men with limited alternative prospects. Religious institutions in those districts often subscribe to ideological currents that make militant participation appear meritorious. Family traditions of military or paramilitary service create cultural conditions that normalize violent organizational membership. Historical grievances, often inherited from Partition and from subsequent India-Pakistan conflicts, provide ideological framing for individual decisions. The recruitment networks operate by identifying young men in these districts who are receptive to militant outreach, providing them with the social and material support needed to commit, and integrating them into organizational structures that promise meaning, brotherhood, and historical significance. The state has at no point seriously disrupted these networks, and significant elements of the establishment view the recruitment pool as a strategic asset rather than a national problem.

Specific Case Studies: How the Doctrine Operates in Practice

Three specific cases illustrate the doctrine in operation, each revealing different aspects of how the institutional relationship functions and how it has evolved under pressure.

The first case is the 2001 Indian Parliament attack and its diplomatic aftermath. On December 13, 2001, five gunmen attacked the Indian parliament complex in New Delhi, killing nine people before being killed themselves. Indian intelligence rapidly attributed the attack to Jaish-e-Mohammed and Lashkar-e-Taiba operating in coordination. India responded with the largest military mobilization in its history under Operation Parakram, deploying nearly half a million troops to the Pakistani border. The standoff continued for ten months. During this period, American pressure on Pakistan was intense, and Musharraf made several public commitments to crack down on militant organizations, including a January 2002 speech that explicitly named LeT and JeM and pledged action against them. Some operational disruption did occur. Specific figures were detained. Charitable assets were temporarily frozen. International recognition of the militant infrastructure as a strategic problem increased significantly. But within a year of the speech, the detained figures had been released, the frozen assets had been reactivated under new organizational names, and the operational infrastructure had largely returned to its pre-crisis state. The case demonstrated that even crises that brought the subcontinent to the brink of war could be absorbed by the doctrine without producing structural change.

The second case is the 2008 Mumbai operation and its handling of the operational evidence. The attacks themselves have been extensively documented, but the post-attack management of the evidence is less often discussed and more revealing of how the doctrine functions. The attackers’ sole survivor, Ajmal Kasab, gave detailed accounts of his recruitment, training, and operational direction. Phone intercepts captured the real-time communications between attackers and Pakistani-based handlers, including the voice of Sajid Mir directing specific tactical decisions during the siege. American investigators secured the cooperation of David Coleman Headley, who had conducted the reconnaissance for the attacks, and Headley provided detailed information about LeT’s command structure and ISI involvement. The evidence was as comprehensive as any major terror attack has ever produced. Yet the Pakistani institutional response managed the evidence rather than acting on it. Specific individuals were detained without serious prosecution. Information requests from foreign investigators were responded to with carefully bounded cooperation. The institutional structure that authorized the operation was insulated from the documentary record. Hafiz Saeed gave press conferences. The militant infrastructure continued operating. The Mumbai case became the canonical example of how comprehensive evidence could be produced without producing comprehensive accountability.

The third case is the 2014 Peshawar Army Public School attack and its different reception. On December 16, 2014, Tehreek-e-Taliban Pakistan operatives attacked the Peshawar Army Public School and killed 132 schoolchildren and 17 staff. The attack produced a different response from the Pakistani establishment than the comparable attacks against Indian targets had. The military launched Operation Zarb-e-Azb with new intensity. The Anti-Terrorism Court system was reformed. Military courts were established to try terror cases. Dozens of TTP figures were tried and executed. The institutional response was sustained, serious, and produced measurable degradation of the TTP organizational capacity. The contrast with the response to attacks against India is informative. The same institution that absorbed the Mumbai evidence without significant action was capable of decisive action when it chose to act. The choice not to act against India-focused groups was therefore a choice, not a constraint. The institutional capacity exists. The institutional preferences determine its application. The Peshawar case provides the comparison that makes the deliberate nature of the differential response unmistakable.

These three cases together establish a pattern. When the establishment decides to act against a militant group, it has the capacity to act decisively. When it chooses not to act, the apparent inability to act is performative rather than real. The differential treatment of India-focused groups versus domestic-threat groups is the strongest available evidence of intentional state policy rather than incompetent state response. The institution knows what it is doing. It does what it does because it has chosen to do so.

The Frankenstein Debate: Lost Control or Continued Direction

The contemporary debate about the Pakistan Army-militant relationship turns on a single question: has the establishment lost control of the groups it created, or does it retain sufficient direction to activate and deactivate them as strategic needs change? The two positions are not abstract. They produce different policy implications, different prediction about Pakistan’s future trajectory, and different assessments of what the shadow war can and cannot achieve.

The Frankenstein thesis holds that Pakistan’s militant networks have become autonomous actors who pursue their own agendas, often at the expense of Pakistani state interests. The thesis points to specific evidence. Tehreek-e-Taliban Pakistan, an organization with roots in networks the establishment once patronized, has been waging open war against the Pakistani state for over a decade and has killed thousands of Pakistani soldiers and civilians. The 2007 Lal Masjid siege demonstrated that armed Islamists were willing to confront the state directly when they believed the state had betrayed them. The 2014 attack on the Army Public School in Peshawar, which killed 132 schoolchildren, was conducted by groups whose operational ancestors had been Pakistani assets. The Frankenstein thesis interprets these episodes as evidence that the monsters have turned on their creator, that the establishment has lost the ability to control the violence it produced, and that Pakistan now faces an internal security threat from networks that originated in its own statecraft.

The continued-control thesis holds that the establishment retains differential control over different organizations and that the apparent loss of control is selective rather than systemic. The thesis points to its own evidence. Lashkar-e-Taiba has been remarkably disciplined for over three decades, conducting major attacks against India when the establishment wanted them and abstaining when the establishment did not. JeM’s pattern is more volatile but still suggests that the worst attacks correlate with strategic opportunity rather than autonomous radicalization. The Khalistan groups operate within parameters that the establishment sets. Hizbul Mujahideen has not turned its guns on Pakistani soldiers. The TTP exception is real but does not undermine the broader pattern. The continued-control thesis interprets the historical record as evidence that the establishment has maintained meaningful control over the India-focused groups while accepting that some networks have become genuinely problematic.

The honest answer is that both theses contain significant truth, and that the truth they share is more important than the truth they dispute. The shared truth is that the establishment’s relationship with militant groups varies by organization. The relationship is closer with some groups and looser with others. The closer relationships have produced the disciplined India-focused capability that the establishment values. The looser relationships have produced the autonomous problems that the establishment would prefer not to have. The institutional choice to maintain the closer relationships, despite their costs and despite the risk that they will eventually become looser relationships, reflects the establishment’s calculation that the strategic benefits outweigh the eventual blowback risks.

The continued-control argument, though, is stronger than its critics acknowledge for the specific organizations the shadow war is targeting. LeT’s organizational discipline is not accidental. JeM’s targeting decisions, however violent, have not turned against the Pakistani state. Hizbul’s exile leadership has not destabilized the regions in which it operates. The Khalistan groups have not pursued goals at variance with Pakistan’s diplomatic interests. The disciplined behavior across these four organizations, sustained over decades, is consistent with continued institutional management. The Frankenstein thesis works better as a description of TTP than as a description of the India-focused networks.

The shadow war’s progress is itself a test of the two theses. If the Frankenstein thesis were correct, the elimination of senior leadership in LeT, JeM, Hizbul, and the Khalistan groups would not be especially damaging to the establishment’s strategic interests, because the establishment had already lost meaningful control over those networks. The eliminations would be unfortunate for the individuals concerned but largely irrelevant to Pakistani statecraft. If the continued-control thesis were correct, the eliminations would be deeply damaging, because they would deprive the establishment of the institutional assets it had cultivated over decades. The observed reaction has been somewhere between the two predictions, but closer to the continued-control side. Pakistani official responses to specific eliminations have ranged from denial to minimization to vague pledges of investigation, but they have not been dismissive. The strategic loss is real, even if the establishment cannot acknowledge it publicly.

The internal Pakistani debate about the doctrine, when it occurs, takes place in narrow circles. Some retired officers, particularly those who served outside the ISI directorate, have published memoirs and articles questioning the long-term viability of the proxy strategy. General Asad Durrani, ISI director from 1990 to 1992, co-authored a book with former RAW chief A. S. Dulat in 2018, The Spy Chronicles, which contained candid acknowledgments about the ISI-RAW relationship and the costs of proxy warfare. The book was controversial in Pakistan and produced a court of inquiry against Durrani. Other retired officers have privately expressed similar views, although the public space for such criticism remains constrained. The institutional center of gravity has not shifted. The doctrine remains intact.

The shadow war complicates the internal debate in important ways. If the elimination campaign continues, and if the establishment cannot stop it, the costs of maintaining the proxy infrastructure will rise. The personnel who serve as the proxy infrastructure will increasingly demand security guarantees that the establishment cannot reliably provide. The protection function will become more expensive and less effective. The legitimization function will become more difficult as the front organizations become associated with eliminated leaders. The training function will become harder to sustain as the cadre of available instructors shrinks. The cumulative effect could, over a long time horizon, force a doctrinal reassessment that decades of international pressure could not produce. This is the deeper logic of the shadow war: not the elimination of specific individuals as ends in themselves, but the gradual increase in the cost of the system until the system becomes unsustainable.

Internal Dissent: The Establishment’s Quiet Reformers

The Pakistan Army is not monolithic, and the doctrinal consensus described above has never been universal. Officers and analysts inside the institution have, at various points, argued against the proxy strategy on grounds of effectiveness, cost, ethics, and long-term viability. Their voices have not prevailed, but they exist, and a complete account must acknowledge them.

The most consequential dissent has come from officers who lived through the Afghan jihad and observed its costs. The militant networks that returned from Afghanistan brought back not only operational skills but also social and ideological dynamics that destabilized parts of Pakistani society. The phenomenon known as Talibanization in Pakistan’s tribal areas during the 2000s was, in significant part, a domestic blowback from policies that the establishment had pursued for external reasons. Senior officers who served on the Afghan border during these years observed the dynamics directly. Some of them concluded, in retirement, that the proxy strategy had produced unmanageable internal consequences. Their critiques tend to be muted in public but more direct in private and in formal lectures at staff colleges, where institutional discussion is permitted.

A second strand of dissent has come from officers who view the proxy strategy as militarily ineffective. The argument, made occasionally in defense journals and at internal seminars, is that the strategy has not produced any of its stated objectives. Kashmir has not been wrested from India. India has not been forced to negotiate on Pakistani terms. The international position of Pakistan has worsened over the period during which the strategy has operated. The military costs to Pakistan, including deaths in TTP attacks and economic costs of international sanctions, have been substantial. The argument concludes that the strategy is a strategic failure that persists for institutional rather than analytical reasons. This critique remains marginal but has gained ground in the post-Afghanistan-withdrawal period when American pressure has eased and Pakistan must increasingly justify the strategy on its own merits.

A third strand of dissent comes from civilian institutions, including the foreign service, certain academic networks, and some elements of the political class. The civilian critique of the doctrine is older and broader than the military critique. Civilian analysts have argued for decades that the proxy strategy undermines Pakistan’s diplomatic position, distorts its political economy, and limits its ability to function as a normal state in international affairs. The civilian critique has had limited operational impact because civilian institutions in Pakistan have limited operational influence over national security. But it provides the intellectual reservoir from which a future shift, if one occurs, would draw.

The dissent is not in itself sufficient to produce change. Institutional inertia, factional interests within the establishment, and the absence of an obvious alternative doctrine all sustain the status quo. But the dissent matters because it documents that the establishment is not unanimous, that the doctrine has been contested internally, and that the conditions for eventual change exist within the institution rather than only outside it. The shadow war is among the conditions that may eventually shift the internal balance. As the costs of the doctrine rise, the dissenters’ arguments gain force. The establishment is not capable of rapid doctrinal change, but it is also not incapable of any change. The trajectory is slow and uncertain, but it is not entirely fixed.

A particular form of internal dissent comes from junior officers who serve in operational theaters where the costs of the doctrine become immediate and visible. Officers commanding units in the tribal areas during the TTP insurgency saw their soldiers die in attacks that traced back to networks the institution had once nurtured. Officers serving on the Line of Control during periods of cross-border firing saw the operational consequences of militant infiltration that the institution had supported. These officers do not generally publish their views, but they shape internal institutional culture in ways that accumulate over time. As more officers cycle through operational commands where the doctrine’s costs are visible, the proportion of senior officers who arrived at their positions through such commands increases. The future leadership of the institution will be drawn from the cohort that has lived with the doctrine’s consequences in ways that the founding generation did not. This generational dimension of internal dissent is harder to measure than published critiques, but it may matter more for long-term institutional trajectory.

External developments also contribute to the conditions for change. Pakistan’s economic situation has deteriorated significantly over the past decade, with successive IMF programs, currency crises, and energy shortages constraining the resources available for any policy domain. The proxy infrastructure is expensive to maintain, and the question of whether Pakistan can afford the doctrine in straightforwardly fiscal terms has become more pressing. The international environment has also shifted. China’s influence in Pakistan has grown, and Beijing’s interests are not always aligned with the doctrine. The Belt and Road Initiative investments require security conditions that the doctrine often disrupts. Saudi Arabia’s regional posture has changed under Mohammed bin Salman in ways that have reduced the financial flows historically supporting the militant infrastructure. Each of these external developments is independent of the shadow war but operates in the same direction, increasing the pressures on the doctrine and the costs of its continued maintenance.

What the Shadow War Reveals About the Nexus

The covert elimination campaign that has reached into Pakistani cities since 2021 functions as a diagnostic instrument. By targeting specific individuals in specific places using specific methods, the campaign reveals features of the Army-militant relationship that abstract analysis cannot establish. The pattern of who gets eliminated, where they get eliminated, and how the establishment responds, provides empirical evidence about the relationship’s structure.

The first revelation is targeting selectivity. The shadow war does not target all militants in Pakistan. It targets specific individuals who fit a specific profile: senior leaders or operationally significant figures in organizations with India-directed agendas, who have sheltered in Pakistani territory under conditions of state protection. The selectivity is itself diagnostic. It tells us that the campaign is not about eliminating terrorism in general but about eliminating the specific personnel who serve specific state-sponsored functions. The targets matter because the establishment cultivated them. The targets matter because the establishment will be embarrassed by their loss. The targets matter because their elimination demonstrates that the establishment’s protection function is not absolute.

The second revelation is geographic distribution. The shadow war reaches into specific Pakistani cities with specific frequencies. Karachi is the most active theater, with the largest number of eliminations. Lahore has seen multiple operations including the elimination of senior leadership. Sialkot, Bahawalpur, Sindh’s smaller cities, and Pakistan-administered Kashmir have all been touched. Crucially, Rawalpindi, the city that hosts Pakistan Army General Headquarters and ISI headquarters, has also seen at least one major elimination, the killing of Bashir Ahmad Peer in February 2023. The geographic distribution maps onto the relationship spectrum. The places where the establishment’s protection is densest are the places where eliminations are rarest, but they are not impossible. The shadow war has demonstrated reach into the heart of the protected zone. The garrison city of Rawalpindi is the case study that makes the point unavoidable.

The third revelation is timing patterns. Eliminations have not occurred randomly. They have clustered in specific periods, particularly in 2023 and 2026, with intervals between clusters that suggest operational rhythm rather than continuous activity. The clustering is consistent with intelligence-driven operations rather than opportunistic ones. The intervals suggest that the campaign moves at the pace of intelligence development and operational opportunity, not at the pace of available personnel or political appetite. The clustering also suggests that specific phases of the campaign have specific objectives. The 2023 cluster eliminated several mid-tier figures. The 2026 surge has reached more senior leadership. The progression is not random.

The fourth revelation is institutional response patterns. The Pakistani establishment’s response to eliminations has been remarkably uniform across cases. Local police announce investigations that produce no public results. Senior officials issue vague condemnations that do not name suspects. Media coverage is permitted but kept within narrow bounds. International blame attribution shifts among various actors, including India, the United States, hostile internal factions within Pakistan, and unspecified anti-state elements. The uniformity of the response pattern is itself diagnostic. It indicates that the establishment has a standard institutional protocol for managing these events, and that the protocol is designed to minimize political damage rather than to identify perpetrators. If the establishment genuinely sought to identify the killers, the investigations would look different. They would produce public results, name suspects, present evidence, and progress over time. They have not, and the absence of progress is consistent across cases.

The fifth revelation is the protection-failure analysis. Each elimination demonstrates a specific failure in the protection apparatus. The figures killed have, in nearly every case, been individuals whose location and routine were ostensibly known to Pakistani security services. They lived in known residences. They had known patterns. They moved in known areas. The fact that they were nonetheless reachable demonstrates that the protection apparatus is not impenetrable, and the reach of the shadow war into different cities demonstrates that the failure is not localized. The implications are uncomfortable for the establishment. Either the protection apparatus is weaker than the establishment had assumed, or the apparatus is being penetrated through specific vulnerabilities that have not been closed, or the protection itself has been compromised at an unknown level. Each possibility is bad for the establishment, and the establishment cannot publicly investigate the question without acknowledging the underlying problem.

The sixth revelation is the deterrent effect on surviving leadership. The behavioral changes among senior militant figures since the shadow war began are observable. Public appearances have declined. Predictable routines have been altered. Travel has been restricted. Communications have been tightened. Security details have been expanded. The changes impose operational costs on the organizations themselves, since leaders who cannot move freely cannot direct operations effectively. The shadow war does not need to kill every leader. It needs to make every surviving leader too constrained to lead. The behavioral changes suggest that this secondary effect is being achieved.

The cumulative implication is that the shadow war is not merely killing individuals. It is exposing the structural features of the Army-militant relationship that the establishment has historically maintained beneath the surface. By forcing the establishment into observable behavior patterns, the campaign generates the empirical evidence that abstract analysis cannot produce. The campaign is, in this sense, a research program as well as a counter-terror operation. Each elimination teaches the analytical community something about how the relationship works, what the protection apparatus consists of, where its vulnerabilities lie, and how the establishment responds when its clients are reached. The campaign targeting the establishment’s clients thus serves an epistemic function in addition to its operational function.

The broader strategic implication is that the establishment’s doctrine, which has rested on the assumption that proxy networks could be sustained at low cost while imposing high costs on India, is being inverted. The proxy networks are now being sustained at high cost while imposing diminishing returns on India. The cost asymmetry that made the doctrine attractive is reversing. If the reversal continues, the doctrine itself will eventually become economically unsustainable, even before it becomes politically untenable. The shadow war is the mechanism through which this cost reversal is being engineered. It is not the only mechanism, and it cannot complete the work alone, but it is the mechanism that has produced the most observable consequences in the shortest period.

A further dimension of the shadow war’s diagnostic function is what it reveals about ISI’s institutional limits. The intelligence apparatus that has historically managed the relationship has been exposed as less capable of protecting its clients than the doctrine assumed. The protection function presumed that ISI’s domestic surveillance capacity, its informant networks, its physical security arrangements, and its coordination with police and military assets would be sufficient to keep designated leaders alive in Pakistani territory. The shadow war has demonstrated that these capabilities have gaps that can be exploited by an adversary with sufficient intelligence preparation, sufficient operational discipline, and sufficient willingness to invest in long-term penetration. The exposure of the gaps is itself damaging to ISI’s institutional reputation within the broader Pakistani establishment. ISI’s claim to manage relationships effectively rested on its claim to deliver protection. The protection failures undermine the claim. The institutional consequences of the failures are not yet fully visible, but they cannot be entirely absent. Bureaucracies that fail at their core functions face internal pressure to reform, even when external pressure is absent.

The shadow war has also revealed something important about the human capital that sustains the proxy infrastructure. The eliminated figures have been concentrated in specific organizational tiers. Senior leadership has been touched but not yet substantially depleted. Mid-tier operational figures have been hit hardest. Recruitment-and-training personnel have been among the targeted categories, suggesting that the campaign understands the importance of the pipeline that produces the next generation of militants. The targeting pattern at the human-capital level is consistent with a campaign that aims to disrupt institutional reproduction rather than merely to remove individual threats. If the personnel who train the next cohort cannot be replaced quickly, the cohort itself will be smaller and less capable. If the recruitment-and-radicalization figures cannot be replaced, the recruitment will slow. If the operational planners cannot be replaced, the operational tempo will decline. The campaign appears to recognize these dynamics and to target accordingly.

The reverse-vulnerability dimension of the shadow war is also worth noting. Each elimination demonstrates not only that specific individuals can be reached but also that specific operational pathways exist. The methods used in eliminations, whether motorcycle-borne shootings, vehicle-borne devices, or other techniques, indicate something about the operational capabilities of the actors conducting the campaign. The fact that these capabilities operate inside Pakistani territory implies the existence of supporting networks that ISI’s domestic intelligence has not been able to neutralize. Each elimination thus implies the existence of a small but functional intelligence and operational support infrastructure that operates beneath ISI’s awareness. The cumulative implication is that ISI’s monopoly over operational activity inside Pakistan is no longer absolute. There is now a parallel operational space, smaller in scale but increasingly visible in effect. This dimension of the shadow war’s revelation is potentially the most consequential of all, because it suggests structural changes in Pakistan’s internal security environment that go beyond the specific elimination campaign.

The contemporary moment is therefore one of inflection. The doctrine has not been abandoned, the institutional commitments remain, and the personnel who run the system are still in place. But the conditions under which the system has historically operated are changing in ways that the system has not yet adapted to. The pace of adaptation has been slow. The recognition of the changes has been partial. The institutional response has been defensive rather than transformative. Whether the system can adapt fast enough to remain viable, or whether the conditions are deteriorating faster than adaptation can occur, is the question that the next several years will answer. The shadow war is one factor among several, but it is among the factors that operate directly on the personnel who sustain the system, rather than on the system’s outer layers, and that gives it disproportionate diagnostic value relative to its operational scale.

Current Status and Future Trajectory

The current state of the Pakistan Army-militant relationship is that the doctrine remains intact, the institutional infrastructure remains in place, and the differential modes of engagement continue to operate, but the conditions sustaining the system are eroding faster than the establishment can compensate for them. The shadow war has accelerated the erosion. International pressure, while reduced compared to the post-September 11 peak, has not disappeared. Pakistan’s economic situation imposes its own constraints. The political space for the proxy strategy has narrowed even within Pakistani public discourse, although not enough to produce decisive change.

The trajectory over the next decade will depend on several factors. The shadow war’s continuation or curtailment is one. Indian decisions about whether to continue, expand, or pause the campaign will shape the cost calculus on the Pakistani side. The establishment’s capacity for doctrinal adaptation is another factor. If the institution can absorb costs without changing course, the doctrine will persist. If costs eventually exceed absorptive capacity, change will become inevitable. Pakistan’s broader political and economic trajectory is a third factor. A weaker Pakistan will have fewer resources to invest in the proxy infrastructure, and the institutional center of gravity may shift in response. The international context, including the evolving American posture toward Pakistan and the Saudi position on militant funding, will shape the external constraints.

What is unlikely is rapid or voluntary dismantlement. The doctrine has been institutionalized for too long, the personnel invested in it are too numerous, and the alternative strategies are too difficult to construct quickly. Change, if it comes, will come slowly and reluctantly, and probably not as a single decision but as a series of small adjustments that accumulate over years. The shadow war contributes to this accumulation. It does not produce it alone, and it cannot complete it alone. But it is one of the few external pressures that operates directly on the personnel who sustain the system, rather than on the system’s outer layers. That is its distinctive contribution, and that is why its continuation matters even when individual eliminations seem incremental.

The deeper question is what Pakistan looks like on the other side of doctrinal change, if such change ever occurs. A Pakistan that genuinely abandoned the proxy strategy would have to find different ways of relating to India, different uses for the personnel and infrastructure now devoted to militancy, and different sources of strategic depth. The transition would not be free of cost. The militants themselves, deprived of state support, would not necessarily disappear quietly. The political dynamics within Pakistan would shift in unpredictable ways. The transition could be more dangerous, in some respects, than the status quo. But the status quo is itself untenable in the long run, both because of external pressure and because of internal contradictions, and the question is not whether change comes but when, how, and in whose favor.

For now, the relationship persists. The training continues. The protection holds, mostly. The authorization function operates at lower frequency than in the past but has not ended. The legitimization apparatus remains intact, although under increasing strain. The five-tier spectrum of relationships, from operational control to adversarial, continues to map onto the differential treatment of different organizations. The contemporary Pakistan Army is not the institution that built the system in the 1980s, but it is the institution that has inherited the system, and that has so far chosen to maintain it. Whether the next generation of officers will make the same choice is the open question that the next decade will answer. The shadow war is part of how the question gets answered, but only part. The rest will be decided by the establishment itself, in the slow accumulation of small choices that determine whether an institution can change, or only repeat, what its predecessors built.

Frequently Asked Questions

Does Pakistan’s Army control terrorist groups?

The Pakistan Army’s control over terrorist groups varies significantly by organization. For groups like Lashkar-e-Taiba and specific operations of Jaish-e-Mohammed, the establishment exercises strategic direction with operational autonomy or even closer forms of management. For groups like Hizbul Mujahideen, the relationship is patronage and protection without close operational control. For Khalistan separatist groups, the relationship is largely benign neglect. For Tehreek-e-Taliban Pakistan, the relationship is openly adversarial. A blanket claim that the Army controls all terrorist groups operating from Pakistan is too simple, but a denial that any institutional relationship exists is even less defensible. The relationship is differentiated, calibrated to strategic role, and has been documented across decades of evidence from Pakistani memoirs, foreign intelligence assessments, and academic research.

Which terror groups does the Pakistan Army support?

The most consistently documented institutional relationships are with Lashkar-e-Taiba, Jaish-e-Mohammed, Hizbul Mujahideen, and historically Al-Badr Mujahideen. These four organizations have been the principal instruments of the Kashmir-focused proxy strategy since the late 1980s. Khalistan-focused groups including Khalistan Commando Force and Khalistan Tiger Force have received sanctuary in Pakistani territory, though with looser operational direction. The establishment’s relationship with each varies in form, intensity, and consistency, but the cumulative pattern across these organizations is one of sustained institutional engagement rather than incidental contact.

Has the Army lost control of the groups it created?

The honest answer is partly yes and partly no, depending on which groups one means. The Tehreek-e-Taliban Pakistan, with roots in networks the establishment once patronized during the Afghan jihad, has clearly become an autonomous and adversarial actor. But the India-focused groups, particularly LeT, have remained remarkably disciplined for over three decades, conducting major operations when conditions favored them and abstaining when they did not. The Frankenstein thesis applies more to the domestic-threat side of the proxy ecosystem than to the India-directed side. The two should not be conflated. Loss of control over TTP is real. Continued meaningful direction over LeT is also real.

Why does Pakistan’s military support terrorism against India?

The doctrinal answer, articulated by Pakistani military thinkers from General Mirza Aslam Beg through subsequent generations, is that conventional military disadvantage relative to India makes direct force-on-force confrontation unwinnable, but sub-conventional pressure on India can be sustained at low cost while constraining Indian responses through nuclear deterrence. The strategy has been called strategic depth, asymmetric warfare, and bleeding by a thousand cuts. The objective is to impose ongoing costs on India over Kashmir without triggering escalation that Pakistan cannot survive. The doctrine has produced limited stated objectives (Kashmir has not been altered) but has imposed real costs on India and has allowed the Pakistani establishment to maintain a posture of resistance that domestic political dynamics reward.

Do Pakistani generals personally know terrorist leaders?

The historical evidence indicates that senior officers, particularly those who served during the Afghan jihad and the early Kashmir insurgency, had personal relationships with militant leaders that have persisted across decades. These relationships are documented in memoirs by officers like Pervez Musharraf and Asad Durrani, in academic interviews with retired personnel, and in the operational record of how specific militant figures have been protected, promoted, or quietly dropped over time. The personal relationships are part of the institutional infrastructure, not a separate phenomenon. They have allowed continuity even as specific officers rotate through command positions.

Has any Pakistani military officer admitted to supporting terrorism?

Public admissions have been rare and qualified. Pervez Musharraf, in his memoir and various interviews, defended Pakistan’s support for Kashmiri militancy as legitimate response to Indian intransigence while denying that the support extended to international terrorism. General Asad Durrani, in his co-authored book with former RAW chief A. S. Dulat, made carefully framed acknowledgments about ISI’s relationships with militant networks, although he did not endorse a clear admission of state sponsorship. These public statements have been controversial within Pakistan and have not produced institutional reckoning. The pattern suggests that some officers acknowledge the relationship privately or in retirement but that the institution as a whole remains committed to public denial.

How does the Army-terror relationship differ by organization?

The relationship spectrum runs from full operational control through strategic direction with operational autonomy, patronage and protection, benign neglect, and finally adversarial. LeT sits at the strategic-direction tier, with the establishment shaping its strategic posture but allowing significant operational autonomy. JeM has shown patterns consistent with operational control for specific high-stakes attacks. Hizbul has been protected and patronized without close operational direction. Khalistan groups have been tolerated and sheltered but not closely managed. TTP has been openly suppressed. The differentiation is real, durable, and analytically essential for understanding why different groups behave differently and why the shadow war’s targeting choices matter.

Can the Pakistan Army shut down terrorism if it wanted to?

The capacity question is distinct from the willingness question. The establishment retains substantial coercive capacity, as demonstrated by major military operations against TTP that have meaningfully degraded that organization. If the establishment chose to apply comparable coercion to LeT, JeM, and Hizbul, those organizations would face severe operational constraints. The constraint is not capacity. It is institutional preference. The doctrine that the establishment continues to embrace makes coercion against India-focused groups strategically undesirable, even when international pressure or domestic costs make limited gestures necessary. The capacity exists. The will does not.

What is strategic depth doctrine?

Strategic depth doctrine, in its original formulation by General Beg and later expanded under General Hamid Gul, held that Pakistan’s defensive position required friendly neighbors who could provide rear-area security. In practice, the doctrine evolved to encompass the use of militant proxies as instruments of regional influence and Indian containment. The Afghan dimension, which sought a friendly Afghan government as defensive depth, has been less successful than originally hoped. The Kashmir dimension, which used militant networks to maintain pressure on India, has produced more sustained operational results, though at significant cost to Pakistan itself.

How is the Pakistani military different from other militaries that have supported insurgencies?

The distinguishing features of the Pakistani case are scale, duration, integration with state institutions, and survival despite international pressure. Other militaries have supported insurgencies for limited periods or against specific targets. The Pakistani military has sustained an integrated proxy infrastructure for over four decades, across multiple changes in civilian and military leadership, against multiple international pressure campaigns, and through significant changes in the global strategic environment. The integration of the proxy infrastructure with state institutions, including charitable organizations, religious networks, financial systems, and political parties, is more complete in the Pakistani case than in most comparable historical cases.

What role does ISI play in managing terror groups?

Inter-Services Intelligence functions as the operational arm of the broader establishment’s relationship with militant groups. Within ISI, specific directorates handle different functions: the S-Wing has historically managed the Kashmir operation, the Counter-Intelligence wing handles security matters, and various other components address specific aspects of the proxy infrastructure. ISI’s operational role includes recruitment vetting, training coordination, financial management, communications security, protection arrangements, and political coordination with the front organizations. The agency does not act independently of the broader establishment. It implements decisions taken at higher levels and provides the institutional capacity through which those decisions become operational reality.

How has the shadow war affected the Army-militant relationship?

The covert elimination campaign has imposed direct costs on the relationship by demonstrating that the protection function is not absolute. Senior figures have been killed in cities where the establishment’s protection should have been most effective. Surviving leaders have changed their behavior in ways that impose operational costs. The institutional protocol for responding to eliminations has revealed itself as designed for damage control rather than perpetrator identification. The cumulative effect is that the costs of maintaining the proxy infrastructure are rising while the benefits of the infrastructure are being eroded by the same campaign that increases the costs. The doctrine remains intact, but the conditions sustaining it are changing.

Does the Army-terror relationship extend to international operations?

The historical record indicates that the establishment’s primary focus has been on India-directed operations, particularly in Kashmir, but that the infrastructure has supported activities beyond that primary focus. Khalistan-focused operations in Western countries, including Canada and the United Kingdom, have been enabled by Pakistani territorial sanctuary even when not directly managed by Pakistani intelligence. The 2008 Mumbai attack involved operational planning that extended through Pakistan, the United States (David Headley’s reconnaissance), and the Maldives. The international dimension is real but secondary. The center of gravity of the proxy strategy is Indian-directed.

What does the shadow war tell us about the Army-terror nexus that abstract analysis cannot?

The campaign’s pattern of targeting selectivity, geographic distribution, timing rhythms, and institutional response patterns provides empirical evidence about the relationship’s structure. The fact that targets cluster in specific cities, that protection failures are systematic rather than localized, that institutional responses follow uniform protocols across cases, and that surviving leaders change their behavior in measurable ways, all provide diagnostic information that academic analysis alone cannot produce. The campaign functions, in addition to its operational purposes, as a research program that generates evidence about how the relationship actually works rather than how it is publicly described.

Will the Pakistani military ever genuinely abandon the proxy strategy?

A doctrinal shift of that magnitude is possible but unlikely in the near term. The institutional commitments are deep, the personnel invested in the strategy are numerous, and the perceived alternatives are unattractive. Change, if it comes, will likely come slowly and through accumulated pressure rather than a single decision. The shadow war contributes to the pressure but cannot complete the work alone. International dynamics, internal Pakistani politics, economic constraints, and generational shifts within the establishment will all shape whether eventual change occurs and on what terms.

How does Pakistan respond when its terror infrastructure is targeted?

The institutional response pattern is highly consistent across cases. Local police announce investigations. Senior officials issue vague condemnations. Media coverage proceeds within narrow bounds. International blame is shifted among various actors, with India typically prominent in the accusations but often joined by claims about hostile internal factions, foreign agencies other than India, or unspecified anti-state elements. The investigations produce no public results. No suspects are named. No prosecutions are pursued. The uniformity of the response across cases indicates that the protocol is institutional rather than improvised, and that its purpose is damage control rather than perpetrator identification.

Are there reformers within the Pakistani military who oppose the proxy strategy?

Yes, although they have not prevailed and their public space is constrained. Some retired officers, particularly those who experienced the domestic blowback from the Afghan jihad, have published critiques of the long-term sustainability of the proxy strategy. Some serving officers have, in private conversations and at internal seminars, expressed similar concerns. The civilian critique, from foreign service officers, academics, and political actors, is older and broader. The institutional center of gravity has not shifted, but the dissent exists and forms the intellectual reservoir from which any future shift would draw.

How does the proxy strategy relate to Pakistan’s nuclear weapons?

The two are operationally linked. Pakistan’s nuclear arsenal is not primarily intended to deter Indian invasion but to deter Indian conventional escalation in response to sub-conventional Pakistani provocation. The structure works as follows: Pakistan supports militant attacks on India; India considers retaliation; Pakistan signals nuclear escalation risk; India declines to escalate; the militant attacks continue. The cycle has held since the late 1990s. Without the nuclear deterrent, the proxy strategy would face Indian conventional retaliation that Pakistan could not absorb. Without the proxy strategy, the nuclear arsenal would lack a sub-conventional offensive complement. The doctrine treats the two components as integrated.

What would happen to the militant leaders if the establishment genuinely withdrew protection?

A genuine withdrawal of protection would expose the leadership to multiple threats simultaneously. They would be vulnerable to Indian operations, to international prosecution, to internal Pakistani factions hostile to specific groups, and to economic constraints if their financial flows were genuinely disrupted. The transition itself would be dangerous, both for the individuals and for Pakistani society, because deprived militants do not necessarily disappear quietly. But the withdrawal would also dramatically reduce the operational capacity of the organizations, since the protection function is not optional infrastructure. It is core infrastructure. Without it, the organizations as they currently exist could not continue to function in their current form.

Is the relationship between the establishment and militants getting closer or more distant over time?

The trajectory is mixed. In some respects, the relationship has hardened over decades, with deeper institutional integration and more developed protection mechanisms. In other respects, it has weakened, with the establishment becoming more constrained in what it can openly do, more selective about which operations it can authorize, and more careful about visible proximity to the militants. The shadow war is accelerating the second trend without reversing the first. The relationship is not approaching either complete integration or complete separation. It is in a slow, uneven evolution that the next decade will continue to shape.