The New Face of Al-Qaeda in Pakistan

Publication: Terrorism Monitor Volume: 2 Issue: 19

The September 26 death of Amjad Farooqi, Pakistan’s most wanted terrorist, reveals the new face of terrorism taking shape in the backwoods of Afghanistan and Pakistan. Killed after a five-hour gun battle with security forces in Sindh, Pakistan, Farooqi had a bounty of Rs 20 million (436,205 USD) on his head. At the time, he was wanted for two abortive attempts on President Pervez Musharraf’s life in December 2003 and January 2004 and the murder of American journalist Daniel Pearl.

Authorities had sought Farooqi’s arrest in connection with several other killings, extortion cases and episodes of sectarian violence as well. Less widely known was his role as a hijacker of Indian Airlines flight IC-814 in December 1999. A member of the trans-national terrorist organization Harkat-ul Jihad al Aslami (HuJI), Farooqi had links with al-Qaeda. Moreover, Farooqi was affiliated with Lashkar-e-Jhangvi (LeJ), a group of Sunni extremists spawned by the Pakistan Army and intelligence to counter the growing strength of Shi’as in Sindh in the early 1990s.

Farooqi’s involvement in the assassination attempts on President Musharraf reveals the nature of terrorist coalitions that have emerged in Pakistan since September 11, 2001. After the attempts, the Pakistani army launched an intensive investigation under Corps Commander, X Corps, which evolved into one of the biggest manhunts in recent history. Investigators quickly identified Farooqi as one of the masterminds of the operation, establishing his ties with Libyan al-Qaeda operative Abu Feraj al-Libbi, Omar Sheikh, Maulana Masood Azhar and LeJ. Investigations also revealed that Farooqi had friends within the Pakistan Army, and had knowledge of the president’s security arrangements. [1]

These revelations confirmed suspicions about the nature of Pakistan’s connections with terrorist organizations since the U.S. launched its Afghan offensive in 2001. One of the things that went unnoticed at the height of U.S. operations was the quiet escape of al-Qaeda and Taliban elements into Pakistan. While the foot soldiers went into hiding in the mountains of Waziristan, the senior leadership of these groups sought and found shelter in major cities like Karachi.

Karachi continues to be a safe haven for extremist religious groups like LeJ and terrorist groups like Harkat ul-Mujahideen and HuJI. In fact, HuJI runs 48 seminaries in Karachi. The largest of these, Madrasa Khalid bin Walid, trains more than 500 students at any given point of time. It is the command headquarters of Karachi Muslims fighting the military regime in Burma. Their leader is Maulana Abdul Guddus, a Myanmarese Muslim who fled to India and made his way to Karachi where he received his religious training before leaving for Afghanistan to join the jihad. A large number of his students fought the Northern Alliance during the Afghan wars of the 1990s. Some went to Kashmir with other HuJI members to fight Indian security forces, but none returned to Myanmar or Bangladesh, choosing instead to make Karachi their home. Their collective objective is to turn Pakistan into another Taliban-style country.

Karachi is also home to various sectarian and extreme religious groups that merged with al-Qaeda and Taliban remnants following the U.S. invasion. Karachi’s most notorious sectarian terrorist, Akram Lahori, took over LeJ’s command after its leader Rias Basra was killed in an encounter in early 2002. Lahori was involved in the assassination of several people, including the brother of then Pakistani Interior Minister Moinuddin Haider, and at least two massacres — in Mominpura graveyard in Lahore where 24 persons were killed and at Imambargah Nafaj at Rawalpindi where 11 persons were killed. Lahori’s case provided significant insight into the evolving alliance between sectarian outfits and al-Qaeda. [2] One of his confidants, Naeem Bukhari, was a suspect in the Daniel Pearl murder with links to Yemeni elements of al-Qaeda who took refuge in Karachi after 9/11.

According to Fazl Karim, a LeJ activist from Rahim Yar Khan picked up for questioning three months after the killing of Pearl, al-Qaeda had merged with various sectarian and criminal groups in Karachi to carry out terrorist attacks within Pakistan. Karim held Pearl while two Yemenis slit his throat. The two Yemenis, it was later discovered, were associates of Ramzi Yousef, the main accused in the World Trade Center attack of 1993. Karim remained in police custody for several months and was never charged. His whereabouts are unknown today.

Farooqi represents just one more link in this new alliance, confirming fears that al-Qaeda and other terrorist groups have successfully merged with religious extremists in Pakistan, making them difficult to identify and segregate. [3] More intriguing, however, is the glaring absence of any attempt to capture Farooqi alive. Had such an attempt been planned, security forces would surely have launched a commando operation sometime during the night, so as to capture Farooqi and his associates who were living in a rented house. What happened instead was a pre-planned shoot-out. A senior police official was quoted in a news report as saying the killing of Farooqi was similar to that of Said Akbar in Rawalpindi in 1951. Akbar assassinated Prime Minister Liaqat Ali Khana and was killed moments later by an “angry crowd,” preventing authorities from getting to the bottom of Liaqat’s killing.

Two theories can be drawn from Farooqi’s death. First, his killing could possibly be part of a cover-up by certain elements within Pakistan’s military-intelligence structure involved in the assassination attempts on Musharraf who were afraid Farooqi’s capture might lead investigators to them. Second, Farooqi may have been killed as part of a cover-up on the part of the ruling establishment to put an end to speculations about the veracity of the assassination attempts. Quite a few news reports early this year had raised the possibility of the assassination attempts being stage-managed. Therefore, this possibility cannot be entirely ruled out. But it is the first conspiracy theory which President Musharraf and his spokesmen would like the world to believe. In the days to come, there is sure to be stories in the Pakistan newspapers about Farooqi’s involvement with al-Qaeda and various other sectarian and terrorist groups. Such stories will fit well with the present effort of the Musharraf regime to portray the President as a lone crusader in the war on terror.

But the reality is quite different. President Musharraf inherited a military-intelligence structure which has been supporting and sheltering terrorists since the Afghan jihad in the 1980s. And, despite the perception in western capitals that Musharraf has been battling hard against sectarian and terrorist groups, there is evidence that at best, the General has been vacillating. Take, for instance, his decision after September 11 2001 to ban various terrorist groups and arrest their leaders. Two of the most well-known terrorist leaders at the time were Maulana Masood Azhar of Jaish-e-Mohammad and Professor Hafiz Sayeed of Lashkar-e Taiba. Both were placed under house arrest but only charged under the Maintenance of Public Order, a prohibitory statute which provides for a three-month preventive detention. Both could easily have been charged under the terrorist act and tried in special terrorist courts.

The Daniel Pearl murder case provides another critical reference point for analyzing terrorist networks operating in Pakistan today. One of the first suspects in the killing was Sheikh Mubarak Ali Shah Gilani, a radical preacher whom Pearl had wanted to interview. Though Gilani was detained and questioned at length, he was let off without any charges. The reason could be Musharraf’s relationship to Gilani. Musharraf had patronized Gilani in 1966, encouraging him to set up the “Climbers Club of Pakistan,” a front for training the Special Services Group (SSG) commandos in mountain climbing. Members of the unit were used in the 1985-1987 attacks on Indian positions at Bilafond Pass. They successfully captured two intermediate posts before being pushed back. Several others have also been detained and interrogated but none have been charged or tried. A common element among all the accused is their association with organizations active in helping al-Qaeda and Taliban elements regroup in Pakistan.

The ouster of the Taliban and al-Qaeda from Afghanistan gave a new lease on life to various criminal, sectarian and religious groups in Pakistan that were finding it increasingly difficult to survive due to international pressure. The September 11 attack had forced the Pakistan government to ban several organizations, close down their offices and freeze their bank accounts. Many of these groups would have faced a natural death had al-Qaeda and Taliban elements not taken shelter in Pakistan following the U.S. attack on their Afghan strongholds. These groups provided al-Qaeda and other groups with the logistics support to regroup in Pakistan, developing in the process a new coalition of terrorists. Complicating this picture even further is the ambiguous relationship between the Pakistani military-intelligence establishment and these local elements that have now befriended al-Qaeda.


1. Kamran Khan, Faooqi’s Killing Leaves Important Questions Unanswered, The News, September 28,2004

2. According to a report in The Friday Times (May 7, 2002).

3. Suspected Mastermind of Attacks on Musharraf: Top Wanted Terrorist Amjad Farooqi Killed, Daily Times, September 27, 2004.