KARACHI AND THE LONG SHADOW OF 9/11

For Raja Umer Khattab, Karachi changed before the city fully understood what was happening. Moving to the Sindh Police’s specialised unit in early 2002 — later named the Counter Terrorism Department (CTD) — the veteran police officer was deeply familiar with Karachi’s typical violence: primarily deadly sectarian conflicts that seldom utilised explosives.

But the threat rising in the shadow of 9/11, 25 years ago, was unlike anything Khattab and his colleagues had ever faced.

As American firepower ousted the Taliban’s first regime and shattered the Al Qaeda network in Afghanistan, the war spilled across the border. It didn’t stop in Pakistan’s rugged tribal belt; it flowed south into the sprawling, chaotic metropolis of Karachi — quietly at first and then with devastating force.

The city was becoming something its law enforcement agencies had never been trained to confront: a staging ground for “a transnational jihadist war”, says Khattab, a highly decorated officer who recently retired after spending the bulk of his 35-year police career on the CTD frontlines.

While Pakistan’s tribal areas offered sanctuary, Karachi offered reach. Highways connected the port city and the country’s business hub to the rest of the country and its international airport linked to the wider world. Its vast population provided anonymity, while established networks of jihadi groups and madressahs [religious seminaries] supplied contacts, funding, logistics and recruits.

A quarter of a century after the infamous events of September 11, 2001, which launched America’s so-called ‘War on Terror’, Zia Ur Rehman looks back at how those events transformed militancy in Pakistan in general and the city of Karachi in particular. Drawing on his own reporting over two decades and the experiences of recently retired Raja Umer Khattab, one of the frontline police officers involved in counter-terrorism operations, he assesses how the terror landscape has changed in these 25 years…

Then came the attacks. In January 2002, Wall Street Journal reporter Daniel Pearl was kidnapped and subsequently murdered. In May 2002, a suicide bomber targeted a bus carrying French naval engineers outside the Sheraton Hotel. The next month, the US Consulate was struck. Christian institutions came under attack. Other incidents followed in rapid succession.

Investigators immediately spotted the fingerprints of displaced Al Qaeda operatives fusing with local factions. “We realised almost immediately that this was completely different from the violence we knew,” Khattab recalls. “We had to adapt fast, leveraging the deep human intelligence we’d cultivated over years on the sectarian frontlines.”

That distinction would define the next two decades.

Karachi became a place where global jihadist networks, Pakistani militant organisations, sectarian groups, violent political actors and criminal networks intersected — sometimes cooperating, sometimes competing and often becoming difficult to distinguish from one another.

Khattab lists one militant organisation after another that had operated in Karachi: “Al Qaeda, Jundullah, Lashkar-i-Jhangvi [LJ], Sipah-i-Muhammad Pakistan [SMP], Harkat-ul-Mujahideen Al-Alami, the Tehrik-i-Taliban Pakistan [TTP], Ansarul Sharia, Baqiatullah, Al Qaeda in the Indian Subcontinent [AQIS], Islamic State Khorasan Province [SKP], the Zainabiyoun Brigade, Jamaat-ul-Ahrar…”

He pauses and admits that he can no longer remember the names of all the groups he had dealt with over the years. Banned Baloch and Sindhi ethno-separatist groups, including the Baloch Liberation Army (BLA) and the Sindhudesh Revolutionary Army, added another layer to the city’s already volatile militant landscape.

The important story, however, is not simply that militant groups operated in Karachi. It is how the nature of that militancy changed after 9/11.

By 2009, the TTP’s presence had begun to transform Karachi’s militant landscape. The militants displaced from tribal areas by Pakistani military operations did not simply seek refuge in the city. They increasingly established themselves in its urban periphery, particularly in Pakhtun-majority neighbourhoods. Raja Umer Khattab describes the period from 2008 to 2014 as one of “absolute devastation” for Pakistan and Karachi.

THE FIRST DRAGNET

The city soon became the frontline of a high-stakes international manhunt.

Hadi Kakar, a Quetta tea stall owner, remembers September 2002 with vivid clarity. A large number of uniformed police and plainclothes intelligence operatives suddenly converged on Karachi’s Defence area, surrounding a three-story building near his shop.

“Heavy gunfire broke out for hours, but we were completely in the dark,” Kakar recalls. “When police officers stopped by for tea later, they mentioned some Arab militants had been arrested.”

The raid unfolded on the first anniversary of 9/11. The primary target was Ramzi Abdullah bin al-Shibh, a key Yemeni operative who later acknowledged his role as a central planner of the 9/11 attacks.

His capture was part of a sweeping dragnet triggered by Pakistan’s entry into the US-led ‘War on Terror.’ Working alongside America’s Central Intelligence Agency (CIA) and the Federal Bureau of Investigation (FBI), Pakistani security forces spent those early months tracking Al Qaeda operatives who had fled the collapse of the Taliban regime in Afghanistan.

While many believed this influx was a sudden post-9/11 retreat, Al Qaeda’s roots in Karachi ran deep, long before 2001. In 1998, Mohammed Sadiq Odeh, a key player in the US Embassy bombings in East Africa, was arrested at Karachi Airport. Abu Ahmed al-Kuwaiti, Osama bin Laden’s trusted courier, also operated a safe house in the city during those formative years. Post-9/11 operations merely brought these existing ties into the light.

The crackdown on Al Qaeda further escalated after Gen Pervez Musharraf narrowly escaped two assassination attempts in Rawalpindi within two weeks in December 2003. A fierce backlash followed. A group of young militants, radicalised under the influence of two physician brothers accused of having links with Al Qaeda, Arshad Waheed and Akmal Waheed, forged ties with Al Qaeda and formed Jundullah, a group distinct from the Iranian organisation of the same name.

It went on to carry out a series of high-profile attacks, including a 2004 attempt on the life of Karachi’s then corps commander. One of the brothers was killed in a US drone strike in South Waziristan in 2009 and was later eulogised by Al Qaeda in its publications.

Over the next few years, joint intelligence operations systematically dismantled the upper ranks of the Al Qaeda network. High-profile Al Qaeda figures, including Khalid Sheikh Mohammed, Abu Zubaydah, Abu Faraj al-Libi, Mustafa al-Hawsawi, Ahmed Khalfan Ghailani, Naeem Noor Khan and Yonis al-Mauritani were hunted down across the country. Karachi itself yielded crucial captures, including Hassan bin Attash, Ammar al-Baluchi and Walid bin Attash.

Yet, the more the senior leadership was hunted, it also exposed Karachi’s role not just as a refuge but as an urban laboratory, where foreign jihadist doctrine integrated with local networks.

Simultaneously, Khattab recalls, the city endured brutal tit-for-tat sectarian violence, driven by groups such as LJ and SMP, marked by mass casualty attacks — such as the 2006 Nishtar Park rally bombing that decimated the top Barelvi leadership and the 2009 Ashura procession bombing.

THE ARRIVAL OF THE TTP

By the late 2000s, the threat was changing again.

My own journalism and research career began in the shadow of that shifting war, around the time Al Qaeda was strategically bringing disparate Taliban factions operating across the border districts together under the TTP banner in 2007.

By 2009, the TTP’s presence had begun to transform Karachi’s militant landscape. The militants displaced from tribal areas by Pakistani military operations did not simply seek refuge in the city. They increasingly established themselves in its urban periphery, particularly in Pakhtun-majority neighbourhoods.

Khattab describes the period from 2008 to 2014 as one of “absolute devastation” for Pakistan and Karachi. I covered this transformation in Karachi extensively from the ground.

Police officers were hunted in broad daylight along their patrol routes. Militants established control over parts of the city’s peripheral localities, running extortion networks, imposing their own rudimentary forms of justice and targeting polio vaccination teams, educationists and political activists, particularly those associated with the Awami National Party (ANP).

The TTP presence in Karachi was itself fragmented mainly due to the abundance of easy extortion revenue. Factions were organised largely along regional lines, reflecting where militants had originated, including Swat, South Waziristan and Mohmand. These semi-autonomous groups controlled their own areas and revenue streams. During this period, the TTP’s central chief, Mufti Noor Wali, also served as the group’s Karachi chief.

To consolidate their position, TTP factions forged alliances with local jihadist and sectarian groups, particularly the LJ. The TTP could bring manpower, weapons and suicide bombers. Local militants brought something equally valuable: knowledge of Karachi. “Born, raised or deeply embedded in Karachi, these local operatives understood the city’s complex urban geography,” Khattab says.

The cooperation eventually developed into operational coordination involving the TTP, Al Qaeda and foreign militant groups, such as the Islamic Movement of Uzbekistan. Together, they mounted sophisticated attacks on high-value military targets, including the 2011 assault on the Pak Navy base PNS Mehran and the June 2014 attack on the Jinnah International Airport in Karachi.

The airport attack proved to be a major turning point. It triggered Operation Zarb-i-Azb in the tribal areas — crippling the TTP and other Al Qaeda-affiliated militant groups over the following years — while accelerating Karachi’s security crackdown, launched in September 2013. Led by the paramilitary Rangers and supported by the CTD, law enforcement forces systematically dismantled the TTP networks that had taken root across the city.

In his book Inqilab-i-Mehsud, TTP chief Noor Wali acknowledged that the crackdown severely weakened the group’s Karachi operations and led to the deaths of several senior commanders.

FROM ORGANISATIONS TO NETWORKS

By the middle of the 2010s, another change was taking place.

As foreign Al Qaeda operatives moved towards the Afghan border, or were killed or captured through raids, the organisation’s influence did not simply disappear. It left behind local recruits, splinter factions and ideological sympathisers capable of sustaining militant activity in new forms.

In 2014, Al Qaeda leader Ayman al-Zawahiri attempted to formalise these loose elements by establishing AQIS, appointing Asim Umar as its leader — a figure already known locally for his popular conspiracy books on Islamic eschatology and the Dajjal.

According to Khattab, AQIS relied heavily on existing networks in Karachi, absorbing local factions to build its operational core. A key faction was Harkat-ul-Mujahideen al-Alami, which had split from the mainly Kashmir-focused Harkat-ul-Mujahideen (HuM) during the early 2000s. HuM al-Alami had orchestrated several high-profile attacks in Karachi, including the 2002 assault on French engineers and the 2004 bomb blast near a concert featuring Indian singer Sonu Nigam.

While AQIS signalled its ambitions through high-profile actions, such as the attempted 2014 hijacking of a Pakistani Navy frigate, its true impact was structural rather than tactical. Unlike foreign fighters, local operatives possessed deep knowledge of the urban terrain, allowing them to blend seamlessly into the city.

Investigations into individual attacks routinely exposed complex, interconnected networks rather than isolated cells. “An investigation into a single bombing would lead to a completely different organisation or cell,” Khattab explains. Instead of operating in isolation, militant factions built fluid alliances, borrowing personnel, tactics and specialised expertise.

The declaration of the Islamic State (IS) caliphate in Iraq and Syria introduced a competing model of jihadism. Frustrated by Al Qaeda’s perceived caution, some disgruntled TTP leaders, including Daud Mehsud (a TTP militant and a former Karachi policeman), shifted their allegiance to IS. Yet, Khattab maintains that IS never succeeded in establishing a permanent, structured presence in Karachi.

Muhammad Israr Madani, an Islamabad-based researcher on militant ideologies, notes that Pakistan’s jihadist landscape has long been dominated by Deobandi groups, leaving little breathing room for IS’s aggressive Salafism to build a recruitment base. He explains, “Even though Al Qaeda was also Salafi-leaning, it chose not to emphasize its Salafi identity when dealing with local Deobandi groups in the Pakistan-Afghanistan region.”

But the significance of this period lay less in which organisation gained the upper hand than in how militancy itself was changing. The old, hierarchical structures were giving way to looser networks, in which people, money, skills and ideology could move across organisational lines.

THE MILITANT NEXT DOOR

The most unsettling sign of this transformation was that the militant no longer had to come from the borderlands. He could come from Karachi itself.

When I asked Khattab which single event had most shaken the city’s intelligence apparatus, his answer was immediate: the May 2015 massacre in Safoora Goth, when gunmen boarded a bus and killed 45 members of the Ismaili community. “The pressure on us was immense,” Khattab recalls.

For law-enforcement agencies, the attack represented more than another episode of violence. It exposed a fundamental change in the profile of the militant. These were not simply hardened fighters arriving from remote border areas. Khattab says, “We were facing a new kind of militant — educated, urban, professionally employed and socially integrated, who had embraced jihadist ideology while continuing to live within ordinary social environments.”

I had seen signs of that shift myself. I knew university students involved in Islamist campus groups and urban militant networks, such as Hizb ut-Tahrir, who became radicalised, eventually gravitating towards Al Qaeda and other militant factions. Some eventually left Karachi for Afghanistan and the tribal areas, where they took up arms and were killed.

High-profile cases, such as the one of Saad Aziz, an elite business school graduate, and Noreen Leghari, a medical student, exposed a troubling trend of self-radicalised, educated youth, forcing authorities to look more closely at how educated young people were being drawn into militant groups.

At a 2017 conference I attended, senior CTD officials, such as Omar Shahid Hamid, consulted academics, security experts and civil society to build a targeted counter-narrative against campus recruitment.

The Safoora Goth massacre was perhaps the clearest expression of that transformation. The cell behind it, which also killed prominent activist Sabeen Mahmud and targeted several police officers, comprised educated, locally rooted operatives. They maintained operational ties to Al Qaeda while attempting to align themselves with the IS’s rising global brand.

According to Khattab, the subsequent crackdown effectively prevented IS from establishing a sustained presence in Karachi. By 2017, the CTD had also dismantled Ansarul Sharia, a shadowy group composed largely of middle-class, highly educated, young men who targeted security personnel.

The pattern was now unmistakable. The large hierarchical organisations had broken down into concealed, highly localised and self-organising cells.

GLOBAL JIHAD AFTER THE WAR ON TERROR

A quarter-century after 9/11, the global terrorscape forged by the so-called ‘War on Terror’ has evolved into something quieter and far more elusive.

The US has long withdrawn its forces from Afghanistan and the Taliban have returned to power. Years of relentless counterterrorism campaigns, drone strikes, high-profile leadership losses and organisational fragmentation have undeniably weakened Al Qaeda, while its primary rival, IS, has also weathered significant operational setbacks.

Yet, a question remains for regional and international security analysts: has Al Qaeda drifted into permanent irrelevance, or has it simply learned to adapt?

“There are two schools of thought,” argues a diplomat working for a Western mission in Islamabad who studies militant organisations in the region. “Some say Al Qaeda is a spent force, irrelevant to the modern jihadist landscape, while others believe its current position reflects strategic silence and that it will return.”

There are reasons for both interpretations.

The US response to 9/11 battered Al Qaeda, decimating its senior leadership, destroying its safe havens and severely crippling its capacity to launch large-scale global operations. Yet, such experiences also force jihadi organisations to evolve.

The rise and fall of the IS provided a stark lesson. Its attempt to establish and govern a self-declared caliphate brought it into direct confrontation with a vast international military coalition and demonstrated the enormous cost of openly holding territory. For Al Qaeda and its affiliates, long-term survival meant shifting away from territorial governance toward cultivating local ties, preserving clandestine networks and wielding quiet ideological influence.

Meanwhile, the geopolitical landscape around them changed too. Former Al Qaeda allies — such as the Taliban in Afghanistan and Hay’at Tahrir al-Sham (HTS) in Syria — went from being the world’s most wanted terrorist groups to running governments.

This didn’t mean the movement was dying. Instead, it showed that these groups had learned a crucial lesson: surviving and keeping power matters more than pulling off dramatic attacks.

THE QUIET NETWORKS

Nowhere is this tactical shift more alarming than along the volatile Pakistan-Afghanistan border. Following the Taliban’s takeover of Kabul in August 2021, Pakistan’s two border provinces, Khyber Pakhtunkhwa and Balochistan, were hit by a sharp revival of violence.

The Taliban’s success in Afghanistan handed local groups such as the TTP a surge of momentum, ideological validation and safe havens across the border. This cross-border support threatens to erase the hard-won security gains achieved through costly military campaigns, such as Operation Zarb-i-Azb.

Behind this increase in militant activity is a pattern of quiet cooperation. Intelligence reports suggest that the AQIS has closely linked itself with local militant groups, especially the TTP, following the 2022 killing of Zawahiri in Kabul by a US drone strike, an incident that highlighted the Taliban’s breach of the Doha agreement.

This arrangement allows Al Qaeda to maintain its regional influence while helping protect the Taliban regime in Kabul from pressure by Islamabad, Beijing and Western governments, which are demanding action against foreign militants operating from Afghan territory.

A recent UN Security Council report highlighted how closely these groups are now connected. It said that Al Qaeda’s official media house, As-Sahab, issued an explicit endorsement of TTP strikes against Pakistani state assets. More importantly, the report said that the AQIS now functions as the “operational backbone” of Ittihad-ul-Mujahideen Pakistan, an umbrella group led by Hafiz Gul Bahadur, the militant originally from North-Waziristan responsible for some of the deadliest suicide attacks against security forces.

EVOLVING SHADOW OVER KARACHI

To the casual observer, Karachi today feels transformed. Unlike the border provinces of KP and Balochistan, currently enduring a relentless surge of armed violence, Karachi has largely been spared the constant, high-intensity terrorism that defined its recent past.

During its bloodiest years, the metropolis was gripped by daily targeted assassinations, sectarian violence and brazen assaults on strategic installations. The decisive security operation launched in September 2013 effectively shattered the entrenched infrastructure that allowed armed factions to control entire neighbourhoods.

That calm, however, is deceptively fragile.

In 2023, a heavily armed TTP assault team breached the Karachi Police headquarters, triggering an hours-long siege in the heart of the city.

More recently, militants from Jamaatul Ahrar, which recently splintered from the TTP, targeted a Sindh Rangers facility. In a media briefing, senior CTD officer Irfan Bahadur explained how such cross-border attacks depend on hidden local cells. An arrested facilitator and his network provided intelligence, carried out reconnaissance in the city and arranged safe passage for four militants who travelled directly from Afghanistan to attack Karachi.

This reveals the primary takeaway from Karachi’s security history: militant groups function as fluid, adaptive networks rather than rigid structures.

A Karachi-based madressah teacher with past links to jihadist circles explains, “Leaders are killed. Factions splinter. Names are erased or changed, and loyalties trade hands. But personal relationships and extremist ideologies survive every crackdown.”

Detained in 2008 by legendary CTD officer Chaudhry Aslam, who was killed by a TTP suicide bomber in 2014, the teacher was cleared and later aided law enforcers in navigating the city’s jihadi underworld.

He stresses that human intelligence, not brute force alone, is crucial to dismantling the older militant groups. “CTD officers such as late Aslam, Khattab, Bahadur and Hamid spent years building deep informant networks across the city’s jihadi landscape,” he says. “Now that many of those officers are dead, retired or reassigned, some of that institutional memory may have been lost.”

He adds a warning: “The new generation of police officers, many with limited understanding of Karachi’s militant underworld, could face a daunting task if a fresh militant wave strikes.”

This fluid dynamic is precisely what confronted Khattab and other law enforcers after 9/11. It became glaringly obvious during the TTP’s urban expansion and grew even harder to trace as groups adapted into micro-cells linked to Al Qaeda and IS. That frontline duty exacted a heavy toll. Khattab and his family survived two separate assassination attempts over his career.

A quarter-century after the first American bombs fell in Afghanistan, the original ‘War on Terror’ may have ended. However, the underlying ideology and informal networks remain intact. “We won’t see a simple repeat of the post-9/11 years,” Khattab notes, pointing to decades of counter-terrorism operations that dismantled Karachi’s old militant ecosystem — its facilitators, safe houses, funding channels and legacy jihadi groups.

Yet, the threat has simply adapted, transitioning from visible command structures into elusive, decentralised cells. Countering it requires mapping the underlying connective tissue before it ignites again.

“These cells need only a spark,” Khattab warns. “They have simply shifted into the shadows, waiting for the right moment to re-emerge.”

The writer is a journalist and researcher
whose work examines the intersections of
militancy, political violence, faith, migration
and rights across Pakistan. X: @zalmayzia

Published in Dawn, EOS, September 13th, 2026