In the early 1990s, future Pakistani President Pervez Musharraf is an up-and-coming military general, who is in charge of military operations. He is a pupil of Hamid Gul, director of the ISI in the late 1980s and a long-time and open supporter of Osama bin Laden. Around 1993, he approaches Prime Minister Benazir Bhutto with a special plan to undermine Indian forces in the province of Kashmir, disputed between India and Pakistan. As Bhutto will later recall, “He told me he wanted to ‘unleash the forces of fundamentalism’ to ramp up the war” against India in Kashmir. Bhutto gives Musharraf the go-ahead, as she had lost power once before by opposing the Pakistani military and ISI, and “Second time around I did not want to rock the boat.” Musharraf approaches several Islamic organizations and commits them to supply volunteers who could be trained to fight as guerrillas in Kashmir. One group he works with is Markaz Dawa Al Irshad (MDI), founded several years before by followers of bin Laden. The MDI already has a military wing known as Lashkar-e-Toiba (LeT). Musharraf is allowed to use LeT’s fighters for his purposes in Kashmir and elsewhere. Other groups effectively created by Musharraf include Harkat ul-Ansar, later known as Harkat ul-Mujahedeen (see Early 1993). In the following months, the level of violence in Kashmir grows as the militias begin sending their fighters there. Around the same time, Musharraf sees early successes of the Taliban (see Spring-Autumn 1994), and along with Interior Minister Nasrullah Babar, begins secretly supporting them and supplying them. The two policies go hand-in-hand, because the militant groups begin training their fighters in parts of Afghanistan controlled by the Taliban. The Pakistani policy of tacitly supporting these militias and the Taliban will continue until Musharraf takes power in a coup in 1999 (see October 12, 1999), and beyond. [Levy and Scott-Clark, 2007, pp. 239-243]
March 1, 2001: Britain Finally Bans Al-Qaeda
Britain officially bans al-Qaeda and 20 other alleged terrorist groups, including the Pakistani militant groups Lashkar-e-Toiba, Harkat ul-Mujahedeen, and Jaish-e-Mohammed. [Rashid, 2008, pp. 414] Britain is behind the US on al-Qaeda, as the US officially declared al-Qaeda a foreign terrorist organization in 1999 (see October 8, 1999). However, the US will not declare Harkat ul-Mujahedeen a terrorist organization until September 25, 2001, Lashkar-e-Toiba until December 20, 2001, and Jaish-e-Mohammed until December 26, 2001 (see December 20, 2001).
April 2001: A. Q. Khan Linked to Pakistani Militant Group
In April 2001, the Pakistani militant group Lashkar-e-Toiba (LeT) holds its annual public meeting in Pakistan. Pakistani nuclear scientist A. Q. Khan attends the meeting as an honored guest. Accompanying Khan at the podium is Sultan Bashiruddin Mahmood, another Pakistani nuclear scientist who had met with Osama bin Laden the year before (see 2000). He will meet with bin Laden again shortly before 9/11 and advise him on how to build a “dirty bomb” (see Mid-August 2001). [Asia Times, 6/4/2004] French journalist Bernard Henri-Levy, the author of a book about Pakistani militant Saeed Sheikh, will later claim in the Wall Street Journal that Khan was a secret member of LeT. [Wall Street Journal, 2/17/2004] The US will ban LeT after 9/11 because of its involvement in a string of attacks against India (see December 20, 2001). LeT is considered linked to al-Qaeda, and bin Laden addressed the annual LeT meeting by phone in some past years. Hafiz Mohammed Saeed, the founder and leader of LeT, has publicly declared that Pakistan should share its nuclear technology with other Islamic nations, a position also advocated by Khan. In 2002, he will claim that people loyal to his organization “control two nuclear missiles.” [Asia Times, 6/4/2004]
Late 2001-Early 2002: Pakistani Militant Group Helps Al-Qeada Operatives Escape into Pakistan
After US forces conquer Kandahar, Afghanistan, in early December 2001, al-Qaeda leader Abu Zubaida gets Pakistani militant group Lashkar-e-Toiba (LeT) to help al-Qaeda operatives escape from Afghanistan to Pakistan. LeT has already given operatives safe houses in the Pakistani cities of Peshawar and Muzaffarabad, trained them there, and helped them travel to Afghanistan to fight US troops. This is according to US government documents leaked by the nonprofit whistleblower group Wikileaks in 2011. These documents provide some details: 
In 2002, three suspected al-Qaeda operatives are arrested in a safe house in Lahore, Pakistan, run by a LeT member. This person had been helping al-Qaeda operatives and their families move to Lahore. Pakistani officials transfer the three al-Qaeda suspects to US custody, but they release the LeT member. [Express Tribune, 5/12/2011] On December 11, 2001, a Saudi named Abdul Aziz al-Matrafi is arrested by police at the Lahore airport. Al-Matrafi is the director of the Wafa Humanitarian Organization, a non-profit organization that the US officially designated an al-Qaeda front in late September 2001 (see September 24, 2001). Al-Matrafi had been staying at an LeT linked non-profit in Lahore, and LeT provided him with a visa and exit paperwork to leave Pakistan. Al-Matrafi is handed over to US custody several days later, and he will eventually be sent to the US-run prison in Guantanamo. [US Department of Defense, 10/25/2007; Express Tribune, 5/12/2011] A Saudi named Jabir Hasan Mohammad al-Qahtani, a suspected al-Qaeda operative who also works for the Wafa Humanitarian Organization, is captured in Kabul, Afghanistan, in mid-November 2001. He is discovered to possess 16 $100 bills. He will later be transferred to the Guantanamo prison. An intelligence analyst will later note: “There were individuals passing out $100 notes to al-Qaeda fighters fleeing Afghanistan for Pakistan. This may have been a part of the help that LeT provided al-Qaeda members.” [US Department of Defense, 2/11/2005; Express Tribune, 5/12/2011] When al-Qaeda leader Abu Zubaida is captured in Faisalabad, Pakistan, on March 28, 2002 (see March 28, 2002), more than 30 other suspected al-Qaeda operatives are arrested at the same time. These arrests take place in two safe houses in Faisalabad run by LeT. The safe houses are apparently run by Hamidullah Khan Niazi, an educational professor and head of the LeT in Faisalabad. Niazi’s house is raided at the same time, and he and 11 others are arrested. According to media reports shortly after the raid, electronic intercepts show that Niazi’s home phone was used by Lashkar-e-Toiba members to help al-Qaeda. However, Niazi and the others at his house are released several days later. [Observer, 4/7/2002; New York Times, 4/14/2002; US Department of Defense, 11/11/2008] But The Observer reports that local police nevertheless say Niazi’s “apparent links to Zubaida are evidence that Pakistan’s militant Islamic fringe is providing key assistance to al-Qaeda as it tries to regroup.” [Observer, 4/7/2002] In 2003, the London Times will report, “US intelligence says [Lashkar-e-Toiba] smuggled [Zubaida] out of Afghanistan, taking advantage of the fact that police never stop their distinctive Landcruisers, which have tinted windows and Free Kashmir numberplates.” [London Times, 3/30/2003]
As some of the examples above indicate, al-Qaeda operatives are often taken into US custody while LeT members are often let go, even though the US names LeT a terrorist group in December 2001 (see December 20, 2001). This may be due to ties between LeT and the ISI, Pakistan’s intelligence agency. For instance, a 2009 diplomatic cable by US Secretary of State Hillary Clinton will note continued links between the ISI and LeT (see December 2009).
December 13, 2001: ISI-Connected Militants Attack Indian Parliament
The Indian Parliament building in New Delhi is attacked by Islamic militants. Fourteen people, including the five attackers, are killed. India blames the Pakistani militant groups Jaish-e-Mohammed and Lashkar-e-Toiba for the attacks. Twelve days later, Maulana Masood Azhar, head of Jaish-e-Mohammed, is arrested by Pakistan and his group is banned. He is freed one year later. [Agence France-Presse, 12/25/2001; Christian Science Monitor, 12/16/2002] The Parliament attack leads to talk of war, even nuclear war, between Pakistan and India, until Pakistani President Pervez Musharraf cracks down on militant groups in early January. [Daily Telegraph, 12/28/2001; Wall Street Journal, 1/3/2002; Guardian, 5/25/2002] As a result of the rising tensions, Pakistani troop deployments near the Tora Bora region of Afghanistan are halted, allowing many al-Qaeda and Taliban to escape into Pakistan (see December 10, 2001). It appears that Saeed Sheikh and Aftab Ansari, working with the ISI, were also involved in the attacks. [Pittsburgh Tribune-Review, 3/3/2002; Vanity Fair, 8/2002]
December 20, 2001: US Bans Pakistani Militant Group, but It Continues Operating Under New Name
The US officially blocks the assets of Lashkar-e-Toiba (LeT), a Pakistani militant group, and Ummah Tameer-e-Nau (UTN), a Pakistani charity front. [White House, 12/20/2001] LeT has frequently attacked targets in India with the tacit support of the Pakistani government. For instance, LeT took credit for an attack on the Red Fort in Delhi in 2000 that killed three people. [BBC, 3/17/2006] But the US fails to mention Pakistani government support for LeT, particularly long-time support by Gen. Pervez Musharraf, who is now president of Pakistan (see 1993-1994). The Pakistani government officially bans LeT one month later. But the group changes its name to Jamaat-ud-Dawa and continues operating, though less openly than before. It is said to be closely linked to al-Qaeda. The US action comes just days after LeT was implicated in an attack on the Indian parliament (see December 13, 2001). [Asia Times, 6/4/2004] India will blame the group for major attacks in 2003 and 2005 that each kill about 60 people. [BBC, 3/17/2006] UTN was founded by Pakistani nuclear scientists (see 2000). The CIA was aware before 9/11 that UTN had proposed selling a nuclear weapon to Libya (see Shortly Before September 11, 2001), and that two UTN scientists met with Osama bin Laden (see Shortly Before September 11, 2001), so it is not known why the US waited until now to act against it.
2002-January 23, 2004: Pakistan Refuses to Arrest Al-Qaeda Leader Ghul, Who Is Linked to Militant Group Supported by ISI
The US wants al-Qaeda leader Hassan Ghul arrested, but the Pakistani government will not do so, apparently because he is part of a Pakistani militant group supported by the ISI, Pakistan’s intelligence agency. Details and timing are vague, but US intelligence becomes increasingly interested in Ghul. He is believed to be part of al-Qaeda leader Abu Zubaida’s secret network of moneymen and couriers. According to a 2011 article by the Associated Press, the CIA has been pressing the Pakistani government to arrest Ghul “for years.” After 9/11, Ghul hides in Lahore, Pakistan, in safe houses run by the Pakistani militant group Lashkar-e-Toiba (LeT). This group helps many al-Qaeda operatives escape Afghanistan and hide in Pakistan after 9/11, and it even helps Zubaida escape and hide (see Late 2001-Early 2002). However, the ISI refuses to arrest Ghul. The Associated Press will report that “former CIA officers who targeted Ghul said he had ties to the Lashkar-e-Toiba terror group, which had the backing of the ISI.” Eventually, the CIA learns that Ghul plans to meet with al-Qaeda operatives fighting against US forces in Iraq. Ghul is captured in Iraq on January 23, 2004 (see January 23, 2004). However, the Pakistani government is said to be furious that Ghul has been captured, and the US is pressed to return him. The US transfers him to a secret CIA prison instead. [Associated Press, 6/15/2011]
February 22, 2002: Rogue Elements of ISI, Especially Those with CIA Ties, May Be Out of Control
In the wake of the kidnapping of Daniel Pearl and suspected ISI ties to the kidnapping plot, Pakistani President Pervez Musharraf is said to begin a “quiet and massive overhaul” of the ISI. However, one senior military source who once served in the ISI warns, “The biggest problem we have here are the rogue elements in the intelligence agencies, especially those who at some time became involved with the CIA.” The ISI is so used to operating independently that even honest agents may be difficult to control. Many may willfully disobey orders. “Among the more dangerous, sources say, are those who acted as Pakistan’s official liaison between the Pakistan Army and militant groups, such as the Kashmiri-oriented Harkat ul-Mujahedeen and Lashkar-e-Toiba, both of which are on the United States’ list of terrorist organizations. The ISI was also a crucial link between Pakistan and the Taliban in Afghanistan.” [Christian Science Monitor, 2/22/2002] By early 2003, the Financial Times will note that Musharraf’s attempts at reforms have largely been abandoned. An expert on the region comments, “It is no longer a question of whether Pakistan is going backwards or forwards. It’s a question of how rapidly it’s going backwards.” [Financial Times, 2/8/2003]
March 28, 2002: Al-Qaeda Leader Zubaida Is Captured in Pakistani City
Al-Qaeda leader Abu Zubaida is captured in Faisalabad, Pakistan. He is the first al-Qaeda leader considered highly important to be captured or killed after 9/11.
Zubaida Injured during Raid – A joint team from the FBI, the CIA, and the ISI, Pakistan’s intelligence agency, raids the house where Zubaida is staying. Around 3 a.m., the team breaks into the house. Zubaida and three others wake up and rush to the rooftop. Zubaida and the others jump to a neighbor’s roof where they are grabbed by local police who are providing back-up for the capture operation. One of Zubaida’s associates manages to grab a gun from one of the police and starts firing it. A shoot-out ensues. The associate is killed, several police are wounded, and Zubaida is shot three times, in the leg, stomach, and groin. He survives. About a dozen other suspected al-Qaeda operatives are captured in the house, and more are captured in other raids that take place nearby at the same time. [New York Times, 4/14/2002; Suskind, 2006, pp. 84-89] US intelligence had slowly been closing in on Zubaida’s location for weeks, but accounts differ as to exactly how he was found (see February-March 28, 2002). He had surgically altered his appearance and was using an alias, so it takes a few days to completely confirm his identity. [New York Times, 9/10/2006]
Link to Pakistani Militant Group – A later US State Department report will mention that the building Zubaida is captured in is actually a Lashkar-e-Toiba safehouse. Lashkar-e-Toiba is a Pakistani militant group with many links to al-Qaeda, and it appears to have played a key role in helping al-Qaeda operatives escape US forces in Afghanistan and find refuge in Pakistan (see Late 2001-Early 2002). [US Department of State, 4/30/2008]
Rendition – Not long after his arrest, Zubaida is interrogated by a CIA agent while he is recovering in a local hospital (see Shortly After March 28, 2002). He then is rendered to a secret CIA prison, where he is interrogated and tortured (see Mid-May 2002 and After). Throughout his detention, members of the National Security Council and other senior Bush administration officials are briefed about Zubaida’s captivity and treatment. [Senate Intelligence Committee, 4/22/2009 
]
Is Zubaida a High-Ranking Al-Qaeda Leader? – Shortly after the arrest, the New York Times reports that “Zubaida is believed by American intelligence to be the operations director for al-Qaeda and the highest-ranking figure of that group to be captured since the Sept. 11 attacks.” [New York Times, 4/14/2002] But it will later come out that while Zubaida was an important radical Islamist, his importance was probably overstated (see Shortly After March 28, 2002).
Tortured While in US Custody – Once Zubaida has sufficiently recovered from his injuries, he is taken to a secret CIA prison in Thailand for more interrogation. [Observer, 6/13/2004; New York Review of Books, 3/15/2009] One unnamed CIA official will later say: “He received the finest medical attention on the planet. We got him in very good health, so we could start to torture him.” [Suskind, 2006, pp. 94-96, 100] Defense Secretary Donald Rumsfeld publicly vows that Zubaida will not be tortured, but it will later come out that he was (see Mid-May 2002 and After and April – June 2002). [New York Times, 4/14/2002]
March 28, 2002: Alleged Member of Hamburg Al-Qaeda Cell Is Arrested with Abu Zubaida, Sent to Guantanamo
Alleged al-Qaeda Hamburg cell member Labed Ahmed (a.k.a. Ahmed Taleb) is arrested in Faisalabad, Pakistan, as part of a series of raids that also results in the arrest of al-Qaeda leader Abu Zubaida and other suspected al-Qaeda operatives (see March 28, 2002). Apparently, he is in the same house as Zubaida when both of them are arrested. Ahmed is transferred to US custody two months later, and then sent to the US-run prison in Guantanamo, Cuba, on August 5, 2002.
History of Robbery and Drug Dealing – Ahmed is an Algerian in his late 40s. In the early 1980s, he served in the Algerian army for four years. He was found guilty several times of robbery. In the early 1990s, he lived in Italy and was found guilty several times of drug dealing and robbery. From 1994 onwards he lived in Hamburg, Germany, and spent a total of two years in prison for a variety of crimes, including robbery and credit card fraud. He continued to deal illegal drugs. Eventually, he became a radical Islamist and associated with members of the al-Qaeda cell in Hamburg, although when and how this happened is unclear. (Note that in 1995, Hamburg cell member and future 9/11 hijacker Mohamed Atta was investigated for petty drug crimes (see 1995).) [US Department of Defense, 9/16/2005]
Plane Flight with Hamburg Cell Members – On September 3, 2001, Ahmed flew to Pakistan with cell member Said Bahaji, another older Algerian named Ismail Bin Murabit (a.k.a. Ismail Ben Mrabete), and others suspected of links to the Hamburg cell. They stayed in the same hotel when they arrived in Karachi, Pakistan. Information on Ahmed’s travel was uncovered by German investigators (see September 3-5, 2001).
Training and Fighting in Afghanistan, Hiding in Pakistan – According to Ahmed’s 2008 Guantanamo file, Ahmed confesses that he, Bin Murabit, and Bahaji traveled together to the al-Faruq training camp near Kandahar, Afghanistan. There, they met Zakariya Essabar, another Hamburg cell member who had just left Germany (see Late August 2001). Ahmed and Bin Murabit stayed together and trained at a variety of locations in Afghanistan. Later in 2001, they fought against US forces near Bagram, Afghanistan. Ahmed then snuck across the Pakistan border with the help of the Lashkar-e-Toiba militant group, and lived in the same safe house as Zubaida and other militants for about a month before they are all captured. Apparently, Ahmed split up from Bin Murabit at some point, because Bin Murabit is not captured, and it is unclear what happens to him. [US Department of Defense, 4/23/2008] (Note that the contents of these Guantanamo files are often based on dubious sources, and sometimes on torture (see April 24, 2011).) Despite Ahmed’s links to the Hamburg cell and Zubaida, he will be transferred to Algeria on November 10, 2008. It is unknown if he is set free or imprisoned by the Algerian government. [New York Times, 4/25/2011]
