The resurgence has been managed by a South Asian offshoot called Al Qaida in the Indian Subcontinent (Aqis), created by Al Qaida’s top leader, Ayman Al Zawahiri, in 2014 in order to slow advances by rival Daesh militants in the region.
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 organisations.
“They are making a comeback of sorts,” said Saifullah Mehsud, executive director of the Fata Research Centre, which monitors militant groups. “But it’s a different, more localised Al Qaida.”
After the fall of Afghanistan’s Taliban government in 2001, many Al Qaida leaders spilt into northwest Pakistan or attempted to blend 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 Qaida to tap into Karachi’s wealth and network of madrasas in search of recruits and technical expertise — and sparking deadly clashes with Pakistani security forces.
“The core Al Qaida, 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 authorised to speak to the media.
While Pakistani officials remain confident that Al Qaida 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 US commanders in Afghanistan, where there are also signs that elements of Al Qaida are trying to come together. A 48-sq km training camp was discovered in Kandahar province in October, and last month US and Afghan special-operations forces freed a kidnapped Pakistani from an Al Qaida-linked camp in Paktia province.
“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 US-led coalition in Afghanistan. “Ultimately, what we think Al Qaida gets out of this relationship is, if the Taliban can provide them some ungoverned space, that allows Al Qaida space to really conduct their global operations.”
In Pakistan, officials say Al Qaida is also readapting through enhanced alliances with established militant groups, including Pakistani Taliban and Lashkar-e-Jhangvi, a sectarian group.
The coordination comes as Pakistan’s military has stepped up its operations against various militant groups, prompting them to seek out support from Al Qaida “for survival”, said one Pakistani law enforcement official who also spoke on the condition of anonymity.
But officials say that the threat from Al Qaida extends far beyond militant groups rebranding themselves. Instead, they say, Al Qaida is finding new recruits from some unlikely Karachi neighbourhoods.
Although ethnic Pashtuns and foreign fighters have historically formed the backbone of Al Qaida 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.
Counterterrorism officials in Karachi have a list of a several hundred active Al Qaida 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 madrasas and schools, casually preaching Islam before targeting certain students for potential recruitment, officials said.
“Nobody may even know it’s Al Qaida 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 Qaida 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 centred 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 Qaida’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,” said the Pakistani counterterrorism official. “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, when, two years ago, militants tried 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 attack, 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 Qaida different and more dangerous from other militant groups is a disciplined management system,” said Rahimullah Yousufzai, a Peshawar-based expert on militants. “Another dangerous thing is they are always looking to penetrate into the armed forces looking for sympathy.”
US intelligence officials have worried for years about potential links between Al Qaida 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 Qaida. “We don’t go for arrests,” the counterterrorism official said. “We just search through their computer, their things, and then neutralise them.”