The Karachi Project

In a dramatic series of raids in February, Pakistani authorities captured more than two dozen top al Qaeda, Afghan Taliban, and Pakistani Taliban leaders, mostly in Pashtun areas on the outskirts of Karachi, Pakistan’s largest city. The list included Afghan Taliban leader Mullah Omar’s top deputy, Mullah Baradar, whose capture raised hopes that the U.S.-led war in Afghanistan was finally gaining momentum. 

The arrests also sparked a debate in Kabul and Washington over the seeming policy shift on the part of Pakistan, which for years had resisted cracking down on top insurgent leaders despite repeated entreaties from the United States. Some accounts suggested that Pakistan had nabbed Baradar to prevent him from cutting a separate peace deal with Afghan President Hamid Karzai, who was reportedly angered by his arrest.

In fact, NATO sources say, most of the Afghan Taliban frontier leadership — known as the Quetta Shura — had for at least three years been sheltered in Karachi under an ultra-secret program run by the Pakistani security establishment and known as the "Karachi Project." The idea that most of the leadership of Taliban’s was stationed in Quetta was a "smoke screen," a top NATO source told me. "In reality, it’s Karachi Shura," confirmed a top NATO commander.

The origins of the Karachi Project reportedly date back to 2003, when, under intense U.S. pressure, then Pakistani President Pervez Musharraf closed "Forward Section 23," a combo of safe houses and camps in Indian-occupied Kashmir that had provided cover and refuge to top militants. The Karachi branch of Pakistan’s powerful Inter-Services Intelligence (ISI) directorate then became the hub for anti-India activities, the Asia Times has reported, led by a coalition of militant groups including Lashkar-e-Taiba and Harukat ul-Jihad al-Islami, as well as elements of the Karachi criminal underworld. According to a recent account in the Guardian, citing "classified Indian government documents," at least two serving ISI officers played a role in the Nov. 26, 2008, attacks in Mumbai, which were launched from Karachi.

While analysts have for years accused Pakistan’s security establishment of playing a double game with militant groups such as Lashkar-e-Taiba — disavowing responsibility for their actions while retaining them as "strategic assets" to be deployed against India — recent revelations emerging from the interrogation of David Headley, a Pakistani-American accused of complicity in the Mumbai attacks, threaten to blow the game wide open.

In Headley’s telling, Pakistan is finding it increasingly difficult to distinguish between "good" jihadi groups — those that launch attacks in India or Afghanistan — and "bad" ones that wage against the Pakistani state. Indeed, that may have been the motive for the Mumbai assault.

According to the Guardian, Headley "told the investigators that the ISI hoped the Mumbai attack would slow or stop growing ‘integration’ between groups active in Kashmir, with whom the agency had maintained a long relationship, and ‘Taliban-based outfits’ in Pakistan and Afghanistan which were a threat to the Pakistani state."

The Karachi Project works under the direct supervision of the ISI, according to accounts in the Indian press confirmed by multiple sources, and also shelters Daud Ibrahim and Tiger Memon, infamous Indian gangsters accused of orchestrating in the 1993 attacks in Mumbai, as well as the Bhaktbal brothers, cofounders of the Indian Mujahideen, the largest Indian jihadi group.

Whether or not one believes such accounts, it is worth noting that Mullah Baradar was reportedly caught at Khudamul Qurun, a hard-line religious seminary located in an area of Karachi that is under the sway of a major Islamist political party, Jamaat-e-Islami, whose leaders were previously accused of sheltering high-profile al Qaeda leaders like Khalid Sheikh Mohammed, the 9/11 mastermind, and other top al Qaeda leaders. Safe houses like this particular seminary are placed and well protected by the Pakistan security establishment.

A former intelligence chief who is actively monitoring the situation noted, "Over the years, it’s Karachi which has seen more al Qaeda and Taliban activity than anywhere else."