Al Qaeda senior leader Ayman al Zawahiri. (SITE Intelligence Group)

September 21, 2011

Diversified, Not Diminished: Al Qaeda in Pakistan Since 9/11

The death of Osama bin Laden in his Pakistani safe house in Abbottabad in early May signaled for many a close to the al Qaeda chapter of militancy in South Asia. With the movement’s godfather dead, surely the group had lost all potency and relevance. This view is illusory, however, and dangerously so.

The decade since 9/11 has seen a fundamental transmogrification in the militant threats to, and emanating from, Pakistan. Like a virus entering a new host, al Qaeda began mutating to adapt to its new environment when it was forced to flee to Pakistan from Afghanistan in 2001. To the world’s general misfortune, the post-mutation al Qaeda has become more violent, virulent and complex: once a wounded movement, on the run and looking for shelter, al Qaeda in Pakistan has regained strength through the seeds it planted in local affiliated groups, many of which not only benefited from their associations with al Qaeda’s fugitive veterans, but also were instrumental in the reconstitution of the movement as a regional and global threat. While al Qaeda’s core functionaries no longer pose the same menace they did on September 11, their success in unifying and internationalizing capable regional terror organizations under their banner has more than made up for al Qaeda’s own diminished capacity.

Surviving the Lean Years

After fleeing the American assault on its Afghan havens, al Qaeda fighters and senior leaders fled east to Pakistan. Many of al Qaeda’s rank-and-file took shelter with friendly tribes in Pakistan’s Federally Administered Tribal Areas (FATA), while some of its senior leadership hid in Pakistan’s large cities. Many of those sheltering in urban centers were later captured with the assistance of Pakistani authorities, including 9/11 mastermind Khalid Sheikh Muhammad, Ramzi bin al Shibh and Abu Zubaydah. By 2004, U.S. officials believed they had captured or killed two-thirds of al Qaeda’s original senior leadership.[1] In addition, a war-scare between India and Pakistan in December 2001 resulting from an attack on India’s parliament building by Jaish-e-Mohammad (JeM) and Lashkar-e-Taiba (LeT) led to Pakistan announcing a ban on extremist groups, including JeM and LeT. A Pakistani crackdown helped reduce cross-border militant infiltration, at least for a time (there is no evidence, however, that Pakistan has severed its ties to, or significantly restricted the activities of LeT, and various front groups established thereafter, including Jamaat-ud-Dawa).[2]

The fight against militant Islamist organizations appeared to be advancing, but success was fragile and fleeting. Al Qaeda showed great resilience in its command structure and replaced operatives and leaders with remarkable speed, bringing to the fore a new generation of al Qaeda leaders that were just as ruthless as their predecessors. The Pakistani terrorist groups banned by General Pervez Musharraf’s government in 2002 re-established themselves under new pseudonyms and with a greater sense of bitterness towards the Pakistani state. This sense of collective victimization, and anger at Pakistan’s cooperation with the U.S., would soon bring organizations like JeM and Lashkar-e-Jhangvi (LeJ) in line with al Qaeda, which had already declared war against the Pakistani state. In addition, al Qaeda fighters in the FATA, particularly in Waziristan, partnered with Afghan insurgents and Pakistan’s nascent Taliban movement and played a role in the Taliban resurgence inside Afghanistan, which started in 2003-04 and gathered momentum in 2006. Al Qaeda fighters cooperated with, trained, and fought alongside Taliban militants launching cross-border attacks into Afghanistan.  Al Qaeda assisted and encouraged the Afghan Taliban in the adoption of suicide bombing and the Taliban made heavy use of al Qaeda’s propaganda machinery and expertise.[3]  

After months of urging from the U.S., and an assassination attempt on Musharraf, Pakistani government forces moved into South Waziristan in the FATA in 2003-04 to disrupt cross-border infiltration and hunt al Qaeda fighters.[4] The Pakistani Taliban, with the help of foreign al Qaeda fighters, rose up against the government and began the first in several rounds of brutal fighting. Government forces fared poorly and in April 2004 signed a peace deal with Taliban leader Nek Muhammad Wazir. The deal was abrogated when Wazir was killed months later in a U.S. drone strike, but subsequent peace deals followed periods of hostilities. By 2006, the Pakistani military had similar agreements with the main insurgent groups in North and South Waziristan. The deals stipulated that the tribes agree to live peacefully and register any “foreigners” living in their areas with the government. The registrations never happened and the government never enforced the provisos; the Taliban’s prestige grew and al Qaeda was able to shelter and operate in the region unhindered.

The Tide Turns

The watershed moment for militancy in Pakistan came in 2007 with the siege of the Lal Masjid, or Red Mosque. Pakistani forces in Islamabad surrounded and later stormed a radical madrassa in the center of Islamabad that had taken on the state and that the government accused of having links to al Qaeda. The widely-televised siege outraged militant Islamists and their sympathizers, and terrorist groups in Pakistan unleashed a wave of attacks across the country, the most prominent of which resulted in the assassination of former Pakistani Prime Minister Benazir Bhutto.

The siege caused different militant groups to tighten ranks and many, previously wavering between obedience to their former masters in the military establishment and adherence to the larger "global jihad” movement, chose to ally with the Taliban and al Qaeda. Baitullah Mehsud launched the Tehrik-e-Taliban Pakistan (TTP) in December 2007, stringing together previously disparate Taliban movements across the FATA into a united insurgency bent on fighting the Pakistani state. Punjab-based LeJ and JeM, groups with a long history of perpetrating sectarian violence inside Pakistan and attacking neighboring India, forged close bonds with the TTP based on their common enmity towards the state, shared belief in the global jihad and their comparative advantages—LeJ, for instance, had technical skills and network support inside Punjab the TTP lacked, while the TTP offered the manpower and physical infrastructure.[5] Harkat-ul-Jihad-al-Islami (HuJI), another group left in the wake of Pakistan’s shift from supporting separatists in Kashmir, also relocated to Waziristan in 2007 and its leader, Ilyas Kashmiri, soon became one of al Qaeda’s top operatives. Kashmiri played a key role in an al Qaeda-approved plot, uncovered in 2010, to launch commando-style raids across major European cities.[6] He also reportedly helped mastermind the 2008 Mumbai attacks carried out by Lashkar-e-Taiba (LeT), which scuttled increasingly productive India-Pakistan peace talks.[7]

LeT, long the darling of the Pakistani security establishment because of its stanch obedience, also began straining at the bit. In 2006, after a lengthy delay, LeT joined other militant groups in attacking coalition troops in Afghanistan.[8] While LeT’s leadership and core movement desists from attacking the Pakistani state, some of its low- to mid-level operatives who shared the al Qaeda worldview grew increasingly frustrated with the constrictions LeT leaders placed on their activities—an inevitable result of LeT’s increasingly close links to al Qaeda and other militant groups in Pakistan—and began to freelance outside of the group’s authority. Such operatives have trained with and provided “manpower and logistical support” to the TTP and other groups attacking the state.[9]

The Haqqani Network, arguably Afghanistan’s deadliest insurgent group, has the longest history of cooperation with al Qaeda and has cultivated perhaps the most symbiotic relationship with the group. When al Qaeda fled Afghanistan in 2001, the Haqqani Network provided it with the nest inside North Waziristan in which al Qaeda could heal itself. Al Qaeda reciprocated with technical skills and training that helped make the Haqqani Network Afghanistan’s most feared insurgent organization. The activities of the two groups grew increasingly intertwined over time, especially under the leadership of Sirajuddin Haqqani—the son of founder Jalaluddin—who shares al Qaeda’s global jihad ideology.[10] As the Haqqanis have grown more powerful, their senior leadership has become inseparable, if not indistinguishable, from al Qaeda’s. Drone strikes targeting al Qaeda operatives in North Waziristan frequently kill Haqqani fighters and commanders. Even today, al Qaeda activity in Afghanistan is heaviest in areas where the Haqqani Network dominates.[11]

Al Qaeda’s Restructuring

Through the killing and capturing of many of its top leaders, and the dispersion of others attempting to avoid a similar fate, al Qaeda in Pakistan lost its strongly hierarchical and bureaucratic command structure. This flattening of the leadership structure has not, however, made the organization impotent. The liquefaction of al Qaeda’s command pyramid not only allowed the network to survive but also increased the lethality of the many other militant organizations now impregnated with al Qaeda operatives.

By embedding its operatives in local terrorist groups and insurgent organizations, al Qaeda was selling its brand cachet and technical expertise in exchange for protection and the resources it needed to continue to operate and fight. Local groups, apart from being ideologically aligned with al Qaeda, craved the importance and recognition afforded by their affiliation and thrived on the technical skills and training that al Qaeda operatives possessed.

The result was to draw together disparate militant groups. Contact with al Qaeda in effect homogenized the ideologies of the different movements. The increase in drone strikes and military operations in Pakistan intensified the siege mentality and inter-dependence of the various groups. Experienced operatives like Ilyas Kashmiri became part of al Qaeda’s inner circle, providing al Qaeda with a deep bench with which to plug gaps created by the death of top leaders. This diversified talent pool helped to supplement al Qaeda’s dwindling core.

Today, groups like the TTP, LeJ, JeM, HuJI, the Haqqani Network, the various Uzbek movements and, increasingly, LeT, cooperate to such an extent that the dividing lines among them have gradually become illusions at best and fabrications at worst. Once local groups, following al Qaeda’s lead, now aspire to act globally and against a broader target set. The TTP, which previously never showed an inclination for attacking targets outside of the region, carried out the Times Square bombing attempt in 2010. In concert with the Haqqani Network and al Qaeda, the TTP also launched a suicide attack on a CIA base in Khost, Afghanistan, in 2009, killing several top agents.

While the network has surely suffered heavy blows with the deaths of Osama bin Laden and dozens of other top leaders over the years, it has retained its vitality and survivability. Although personally diminished, al Qaeda’s core group has found new ways of expanding its lethality: it has succeeded in innervating other groups with the means to conduct violence in its name, causing the brand to supersede individual membership in importance. While al Qaeda’s traditional structure has deteriorated over the years, the threat emanating from Pakistan to the region, and the world, is diversified rather than diminished. Ten years on, the time for vigilance is not yet past.

[1] Faye Bowers, “Al Qaeda’s New Young Guard: A Shift in Tactics,” Christian Science Monitor, February 13, 2004. Available at
[2] Following the ban and the India-Pakistan peace process that followed, Indian officials publicly admitted that cross-border infiltration from Pakistan had been considerably reduced, even as late as 2006.
K. Alan Kronstadt, “Pakistan-U.S. Relations,” CRS Report for Congress, July 27, 2006. Available at
“Pakistan hails PM’s remark,” Times of India, March 26, 2006. Available at
“Pakistan,” Ministry of Defence, Government of India Website. Available at (accessed on September 13, 2011).
[3] Seth Jones, In the Graveyard of Empires: America’s War in Afghanistan (July 2009), pg. 137, pp. 262-263
[4] Ahmad Rashid, Descent into Chaos: The Unites States and the Failure of Nation Building in Afghanistan, Pakistan and Central Asia, (June 3, 2008), pp. 269-272
[5] Frederick W. Kagan and Ahmad Majidyar, “Punjabi Taliban,” AEI Critical Threats, May 28, 2009. Available at
[6] Duncan Gardham and Raveen Swarmi, “European terror attacks mastermind sent operative to Britain to raise arms and money,” The Telegraph, October 17, 2010. Available at
Duncan Gardham and Robert Crilly, “Bin Laden ‘personally approved’ attacks on Europe,” The Telegraph, October 1, 2010. Available at
[7] Pakistani journalist Syed Saleem Shahzad, the only journalist known to have interviewed Kashmiri, made these allegations in a book that was being readied for publication when Shahzad was kidnapped and murdered under suspicious circumstances. The book has been published posthumously.
Syed Saleem Shahzad, Inside Al-Qaeda and the Taliban: Beyond Bin Laden and 9/11 (Pluto Press, 2011).
[8] Stephen Tankel, “Lashkar-e-Taiba in Perspective,” New America Foundation, February 2010. Available at
[9] Stephen Tankel, “Lashkar-e-Taiba in Perspective,” New America Foundation, February 2010. Available at
[10] “Ansar al-Mujahideen Hosts Open Meeting with Sirajuddin Haqqani,” SITE Intelligence Group, May 6, 2010. Available at
[11] Don Rassler and Vahid Brown, “The Haqqani Nexus and the Evolution of al-Qa’ida,” CTC Sentinel, July 14, 2011. Available at
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