Pakistani security officials with Naeem Bokhari, allegedly part of a joint terrorist network of al-Qaeda in the Indian Subcontinent, Lashkar-e-Jhangvi and the Pakistani Taliban, in Karachi on Feb. 12, 2015. (European Pressphoto Agency)

Five years after most senior al-Qaeda leaders are thought to have fled this port city, officials in Karachi worry that the organization is regrouping and finding new support here and in neighboring Afghanistan. They are especially concerned about the recruitment of potential foot soldiers for the next major terrorist attack.

The resurgence has been managed by a South Asian offshoot called al-Qaeda in the Indian Subcontinent (AQIS), created by al-Qaeda’s top leader, Ayman al-Zawahiri, in 2014 in order to slow advances by rival Islamic State militants in the region.

[A closer look at Ayman al-Zawahiri]

Initially, AQIS struggled to gain traction in Pakistan — it has been the principal target of President Obama’s drone-strike strategy in the country’s northwestern tribal belt. But AQIS is now finding its footing in southern Pakistan, powered by fresh recruits and budding alliances with other militant organizations.

“They are making a comeback of sorts,” said Saifullah Mehsud, executive director of the FATA Research Center, which monitors militant groups. “But it’s a different, more localized al-Qaeda.”





After the fall of Afghanistan’s Taliban government in 2001, many al-Qaeda leaders spilled into northwest Pakistan or attempted to blend in in Karachi, a bustling city of more than 20 million residents. A significant number of those core leaders were eventually killed or captured, or fled to the Middle East, officials said.

But the formation of AQIS is again allowing al-Qaeda to tap into Karachi’s wealth and network of madrassas in search of recruits and technical expertise — and sparking deadly clashes with Pakistani security forces.

“The core al-Qaeda, the thinkers and planners, are not coming to the front right now, but they are giving directions, and . . . the local boys are going in big numbers,” said one counterterrorism official in Karachi who asked to remain anonymous because he was not authorized to speak to the media.

While Pakistani officials remain confident that al-Qaeda probably can’t pull off another 9/11-style attack on the United States, there is concern that the group is, as one official put it, “planning something big.” The official added that it is unclear, however, whether such an attack would be aimed at Pakistan, another country in South Asia or the West.

Those concerns mirror assessments from U.S. commanders in Afghanistan, where there are also signs that elements of al-Qaeda are trying to come together. A 30-square-mile training camp was discovered in Kandahar province in October, and last month U.S. and Afghan special operations forces freed a kidnapped Pakistani from an al-Qaeda-linked camp in Paktia province.

[‘Probably the largest’ al-Qaeda training camp ever is destroyed]

“They are looking to nestle in with the Taliban so they have some level of sanctuary,” said Brig. Gen. Charles H. Cleveland, chief spokesman for the U.S.-led coalition in Afghanistan. “Ultimately, what we think al-Qaeda gets out of this relationship is, if the Taliban can provide them some ungoverned space, that allows al-Qaeda space to really conduct their global operations.”

In Pakistan, officials say al-Qaeda is also re-adapting through enhanced alliances with established militant groups, including the Sunni-dominated Pakistani Taliban and Lashkar-e-Jhangvi, a sectarian group that had been focused on attacking Shiite Muslims.

The coordination comes as Pakistan’s military has stepped up its operations against various militant groups, prompting them to seek out support from al-Qaeda “for survival,” said one Pakistani law enforcement official who also spoke on the condition of anonymity.

But officials say that the threat from al-Qaeda extends far beyond Sunni militant groups rebranding themselves. Instead, they say, al-Qaeda is finding new recruits from some unlikely Karachi neighborhoods.

Although ethnic Pashtuns and foreign fighters have historically formed the backbone of al-Qaeda in the Afghanistan-Pakistan region, some ethnic Bengalis and other Urdu-speaking Mohajirs — Muslims who migrated to Pakistan from India after the 1947 partition — are also being lured into the group, officials said.

“They are not into this factional fighting, or fighting with other sects or Shiites, but they will go for enforcement of sharia law overall” and be drawn to al-Qaeda sermons against the West, the official said.

Counterterrorism officials in Karachi have a list of several hundred active al-Qaeda members, which makes them assume there are at least a few thousand on the streets.

In Karachi, AQIS has divided itself into three operational segments — recruitment, financial and tactical — made up of four-to-six-person cells.

The recruitment cells work in madrassas and schools, casually preaching Islam before targeting certain students for potential recruitment, officials said.

“Nobody may even know it’s al-Qaeda operating,” said Saad Khan, a retired Pakistani intelligence officer.

Cells solicit local businesses for donations, often under the guise of supporting Islamic charities, officials said. Officials have no estimates for how much money al-Qaeda raises from relatively wealthy Karachi but said that militants are often found carrying hundreds of dollars in cash.

“They are being told they don’t need to do any job and they don’t need to indulge in petty crimes,” the counterterrorism official said. “But they are told they have to remain very discreet.”

Although such discretion complicates the work of counterterrorism officials, they think that the Karachi cells are just spokes in a broader operation centered near Pakistan’s southwestern border with Afghanistan or Iran.

From Karachi, AQIS tactical cells ferry money and messages to that general area, often moving through Quetta, which is also where part of the Afghan Taliban leadership resides, officials said. From Quetta, militants cross the border into Afghanistan but appear to have little knowledge about al-Qaeda’s broader ambitions or tactics in the region, intelligence officials said.

“The people we come into contact with say they go to Afghanistan but are put into a small corner and remain there and can’t go out,” the Pakistani counterterrorism official said. “Then they get direction from there, from another Pakistani, and return.”

In Pakistan, officials said AQIS has been linked to just one major attempted terrorist attack — an effort two years ago to hijack a Pakistani navy vessel from the port of Karachi.

The attack was foiled, but five Pakistani navy officers were convicted of helping to orchestrate the operation, according to media reports.

AQIS militants have also been linked to several recent police killings in Karachi. Officials say they are targeted revenge attacks or the early stages of a larger plot to try to weaken the morale of security forces.

“What still makes al-Qaeda different and more dangerous from other militant groups is a disciplined management system,” said Rahimullah Yusufzai, a Peshawar-based expert on militants. “Another dangerous thing is they are always looking to penetrate into the armed forces looking for sympathy.”

U.S. intelligence officials have worried for years about potential links between al-Qaeda and rogue Pakistani military officials. That Osama bin Laden was found hiding near a Pakistan military training academy did little to allay their suspicions.

Pakistani security and intelligence agencies, however, seem to have no tolerance for the modern-day al-Qaeda. “We don’t go for arrests,” the counterterrorism official said. “We just search through their computer, their things, and then neutralize them.”

Last month, police in Pakistan’s Punjab province reported killing 14 al-Qaeda militants, including the group’s leader there, over two days in “encounters” with police. Pakistan’s Dawn newspaper reported that the suspects had been in police custody for four months before they died.

Saad Muhammad, a retired Pakistani general, said Pakistan’s military is determined not to allow AQIS to jeopardize its recent gains against Islamist militant groups.

“You can’t say they will be totally naked, but they will not be able to gain strength in any significant way,” Muhammad said.

But Syed Tahir Hussain Mashhadi, a retired Pakistani army colonel and sitting senator, said the real concern remains how a city such as Karachi fits into al-Qaeda’s broader global ambitions. The answer to that, he said, remains murky.

“Al-Qaeda is just an umbrella, and the top of the pyramid is what is controlling and enduring,” he said. “They don’t have to put much effort into Pakistan because all they have to do is pick up all these existing, bloodthirsty splinter organizations and they have a ready-made killing machine.”

Nisar Mehdi in Karachi, Aamir Iqbal in Peshawar and Antonio Olivo in Kabul contributed to this report.

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