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).
Late 2001-Spring 2002: European Intelligence Agencies Monitor Al-Qaeda Relocating in Pakistan
In September 2002, shortly after the arrest of al-Qaeda leader Ramzi bin al-Shibh in Karachi, Pakistan (see September 11, 2002), the New York Times will report: “Even before Mr. bin al-Shibh’s arrest, European officials warned that al-Qaeda appeared to have shifted much of its operations in Pakistan to Karachi. A year ago, 90 percent of communications and other links between suspected al-Qaeda members in Europe and individuals in Pakistan were traced to the city of Peshawar, near the Afghan border, a European law enforcement official said. As of this spring, roughly half of intercepted communications and other links were being traced to Karachi.” A European diplomat comments, “Obviously the brains and money for the terrorists have shifted from Peshawar to Karachi.” [New York Times, 9/15/2002] Presumably many of the communications to Peshawar involve al-Qaeda leader Abu Zubaida, considered a key communications hub and who has been monitored by a number of intelligence agencies, including the French, since at least 1998 (see October 1998 and After). Zubaida moves from his long-time base in Peshawar to the Pakistani city of Faisalabad after 9/11 and is captured there in March 2002 (see March 28, 2002). Al-Qaeda leaders Khalid Shaikh Mohammed and Ramzi bin al-Shibh are interviewed in Karachi around June 2002, a fact that is quickly shared with US intelligence (see June 14, 2002 and Shortly After).
December 2001-Spring 2002: Pakistani Government Allows Al-Qaeda and Taliban to Regroup in Pakistan’s Tribal Region
In December 2001, al-Qaeda and Taliban forces in Afghanistan are defeated in the battle of Tora Bora, and the survivors generally flee across the border into Pakistan’s tribal region. Many flee into the region of South Waziristan, since it is directly adjacent to Tora Bora and there are no Pakistani government forces guarding the border there (see December 10, 2001). In March 2002, several hundred more militants flee from Afghanistan into South Waziristan after Operation Anaconda (see March 2-13, 2002). They rebuild their central command there, particularly in a remote part of South Waziristan known as the Shakai valley. [New York Times, 6/30/2008] Pakistani journalist Ahmed Rashid will later describe South Waziristan: “With its high mountains, steep slopes, deep ravines littered with broken rock and shale, and its thick forests, it was an ideal hideout. Many of its valleys were virtually inaccessible, except along steep winding paths that required the agility of mountain climbers, and were easy to defend.” [Rashid, 2008, pp. 148, 268] In the spring of 2002, US intelligence begins reporting that large numbers of foreigners are hiding in South Waziristan and neighboring North Waziristan. But Gen. Ali Jan Orakzai, the commander of Pakistani forces in the area containing Waziristan, is skeptical. Born in the tribal region, Orakzai is said to be Pakistani President Pervez Musharraf’s close friend and main adviser on the region. Even in 2008, he will tell the New York Times that he considered the US warnings about al-Qaeda to be mere “guesswork” and that his soldiers “found nothing.” Former US intelligence officials will agree that nothing is found, because they say that Orakzai’s military forces only enter the region in large, slow-moving sweeps that are easily avoided by militants. Robert Grenier, CIA station chief in Pakistan at the time, will later suggest that Orakzai did not want to find the foreigners as this could have caused trouble, including a tribal uprising. Grenier will say, “Orakzai and others didn’t want to believe [the foreigners were there] because it would have been an inconvenient fact.” [New York Times, 6/30/2008]
December 2001: Al-Qaeda Computer Provides Intimate Look at Terror Operations
Alan Cullison, a Wall Street Journal reporter in Afghanistan, obtains two computers looted from an al-Qaeda house in Kabul. One computer apparently belonged to al-Qaeda military commander Mohammed Atef but contained few files. The other had been used mostly by al-Qaeda second-in-command Ayman Al-Zawahiri and had about 1,000 files dating back to 1997. The reporter later gives the computers to the CIA which confirms the authenticity of the files. The computer files reveal how al-Qaeda operates on a day-to-day basis. The files include correspondence, budgets, attack plans, and training manuals. Messages between various al-Qaeda’s offices reveal a fractious, contentious community of terror plotters. There are disputes about theology, strategy, and even expense reports. A montage of 9/11 television reports set to rousing victory reports shows that the computer was used after the attacks. While some of the new information is surprising, for the most part it confirms the claims made about al-Qaeda by Western governments. A letter drafted on the computer in May 2001 confirms that al-Qaeda was behind the assassination of Ahmed Shah Massoud (see September 9, 2001). Other messages shows that the organization orchestrated the 1998 embassy bombings (see 10:35-10:39 a.m., August 7, 1998). However, there is no material relating specifically to the plotting of the 9/11 attacks. [Wall Street Journal, 12/31/2001; Atlantic Monthly, 9/2004]
December 2001: Al-Qaeda-Linked Figures and Indonesian Military Attack Christian Villages on Island of Sulawesi
In October 2000, Agus Dwikarna, an Indonesian militant linked to al-Qaeda, helps establish the paramilitary organization Laskar Jundullah. It is modeled after Laskar Jihad, another paramilitary organization formed earlier (see January 1999-July 2001), except Laskar Jihad draws its recruits from the Indonesian island of Java whereas Laskar Jundullah draws its recruits from the Indonesian island of Sulawesi. Laskar Jundullah gathers about 2,000 recruits to central Sulawesi. Mostly using bats and machetes, they support local Muslims in violent conflicts with Christians near the town of Poso, which have been occurring off and on since 1998, with heavy casualties on both sides. [Human Rights Watch, 12/2002; Conboy, 2003, pp. 223-224] In the second half of 2001, some al-Qaeda linked figures begin helping Dwikarna and Laskar Jundullah: Omar al-Faruq, a Kuwaiti, who is said to be a key go-between for al-Qaeda and Jemaah Islamiyah. Al-Faruq and Dwikarna hosted al-Qaeda second-in-command Ayman al-Zawahiri when he visited Indonesia in 2000 (see June 2000). Syeh Hussein, a.k.a. Rashid, a Saudi. He is al-Faruq’s handler and is said to have access to Osama bin Laden. He is posing as a representative of the Al Haramain Islamic Foundation. Dwikarna is also posing as an Al Haramain employee (see June 2000). [Conboy, 2003, pp. 223-224] Reda Seyam, a.k.a. Abu Daud, an Egyptian. He had fought with al-Qaeda in Bosnia in the early 1990s and also has links to key al-Qaeda figures, including having met directly with bin Laden. He had worked for the Twaik Group, said to be a front for the Saudi intelligence agency, and is in Indonesia working for Rawasin Media Productions, which is also said to be a Saudi intelligence front (see 1995-1998). [Conboy, 2003, pp. 223-224; Chicago Tribune, 3/31/2004]
On December 1, 2001, al-Faruq, Hussein, and Seyam meet with fifty Laskar Jundullah recruits near the town of Poso, in central Sulawesi. They present the recruits with weapons, including high quality M-16s and Uzis (which are very unavailable in Indonesia except from military or overseas sources). Near midnight, the group goes to Sepe, a small Christian village near Poso. They attack the village, burning about two hundred houses and killing an unknown number of people. The attack is filmed using night vision equipment. [Conboy, 2003, pp. 223-224] There are allegations that some Indonesian military units take part in the attack. Since 90% of Indonesia’s population is Muslim, most Indonesian soldiers are Muslim as well. Human Rights Watch will later comment, “there is evidence that [Indonesian] soldiers did engage the attackers in a fight [at Sepe], as three soldiers from Infantry Battalion 711 from Palu were reported in critical condition.” Around this time, Laskar Jundullah forces attack about seven other Christian villages in the region. There are reports the Indonesian military sometimes joins these attacks and at other times fails to help the attacked villages. These attacks are little noticed outside of Indonesia, and the involvement of al-Qaeda-linked figures will not be publicly revealed until later. But there is pressure within Indonesia for the government to do something. More military units are bought in several days after the Sepe attack, and they largely quell the violence. [Human Rights Watch, 12/2002] Around December 4, six suspicious foreign men, believed to be Islamist militants, are detained in the area and then let go. [BBC, 12/4/2001] Later that month, Laskar Jundullah is implicated in a bombing of a Kentucky Fried Chicken restaurant in the city of Ujung Pandang, in southern Sulawesi. The group plans further attacks, but it is divided by internal squabbles. Dwikarna, who was not present in the Sepe attack, is upset at the others for recklessly filming themselves in the attack and then planning to use the footage for propaganda purposes. Seyam will be arrested in Indonesia late 2002 and footage of the Sepe attack apparently will be found with him. Dwikarna will be arrested in 2002 as well. His group, and the violence in Sulawesi, will generally come to an end that same year. [Human Rights Watch, 12/2002; Conboy, 2003, pp. 223-224]
December, 2001: US Congress Fails to Fund Plan to Strengthen Pakistani Government Control over Tribal Region
Pakistani President Pervez Musharraf meets with Wendy Chamberlin, the US ambassador to Pakistan, and asks for US support to help him extend his control over the tribal areas near the Afghanistan border. At the time, al-Qaeda and Taliban forces are being defeated in Afghanistan and fleeing to the tribal region. Musharraf suggests the local people can be bought off with basic government services such as schools, clinics, and roads, and that large cash rewards could be offered to locals who help track down fugitive militants. Musharraf claims he would need $40 million to implement such a plan. Chamberlin agrees, but Congress soon refuses to fund the money, and only gives $14 million for local law enforcement. Charlie Flickner, a Republican clerk on the House Appropriations Committee, successfully lobbies his Republican colleagues not to support it. One anonymous Democrat on the committee will later say: “We blew it. There was a window of opportunity, but we lost it by not funding them adequately.” The tribal areas soon become a strong base for al-Qaeda and the Taliban. [New Yorker, 7/28/2003]
December 2001 and After: Drug Kingpin Let Go by US; Then Rebuilds Drug Network for Taliban and Al-Qaeda
Afghan drug kingpin Haji Juma Khan (see July 2000) is arrested and taken into US custody. Although his role in the illegal drug trade is known to US officials, he is let go. A European counterterrorism expert says, “At the time, the Americans were only interested in catching bin Laden and Mullah Omar.” Another major kingpin is arrested and released around this time as well (see Late 2001). After being released, Khan reestablishes a smuggling network that greatly benefits the Taliban and al-Qaeda. For instance, in May 2004, a tip off will reveal that Khan is employing a fleet of cargo ships to move Afghan heroin out of Pakistan to the Middle East. Some return trips bring back plastic explosives, antitank mines, and other weapons to be used against US troops in Afghanistan. In 2004, Assistant Secretary of State Bobby Charles says of Khan, “He’s obviously very tightly tied to the Taliban.… There are central linkages among Khan, Mullah Omar, and bin Laden.” [Time, 8/2/2004] In 2006, a report by the research arm of Congress will label Khan as one of three prominent drug kingpins with ties to the Taliban and al-Qaeda, but he apparently has not yet been put on the official US list of wanted drug figures. [Congressional Research Service, 1/25/2006]
Early December 2001: Al-Qaeda ‘Puppet Master’ Abu Qatada Disappears in Britain
Al-Qaeda religious leader Abu Qatada disappears, despite being under surveillance in Britain. He has been “described by some justice officials as the spiritual leader and possible puppet master of al-Qaeda’s European networks.” [Time, 7/7/2002] He supposedly escapes from his house, which the police are monitoring, in a minivan with his heavily pregnant wife and four children. [London Times, 10/25/2002; O’Neill and McGrory, 2006, pp. 108] Qatada had already been sentenced to death in abstentia in Jordan, and is wanted at the time by the US, Spain, France, and Algeria as well. [Guardian, 2/14/2002] In October 2001, the media had strongly suggested that Qatada would soon be arrested for his known roles in al-Qaeda plots, but no such arrest occurred. [London Times, 10/21/2001] In November, while Qatada was still living openly in Britain, a Spanish judge expressed disbelief that Qatada hadn’t been arrested already, as he has previously been connected to a Spanish al-Qaeda cell that may have met with Mohamed Atta in July 2001. [Observer, 11/25/2001] Time magazine will later claim that just before new anti-terrorism laws go into effect in Britain, Abu Qatada and his family are secretly moved to a safe house by the British government, where he is lodged, fed, and clothed by the government. “The deal is that Abu Qatada is deprived of contact with extremists in London and Europe but can’t be arrested or expelled because no one officially knows where he is,” says a source, whose claims were corroborated by French authorities. The British reportedly do this to avoid a “hot potato” trial. [Time, 7/7/2002] A British official rejects these assertions: “We wouldn’t give an awful lot of credence [to the story].” [Guardian, 7/8/2002] Some French officials tell the press that Qatada was allowed to disappear because he is actually a British intelligence agent. [Observer, 2/24/2002] It appears that Qatada held secret meetings with British intelligence in 1996 and 1997, and the British were under the impression that he was informing on al-Qaeda (though there is disagreement if he was misleading them or not) (see June 1996-February 1997). Qatada will be arrested in London on October 23, 2002 (see October 23, 2002).
December 4, 2001: Stratcom Report Says US Backed Some Forerunners of Al-Qaeda
The United States Strategic Command (Stratcom) produces a document mentioning that the US backed some of al-Qaeda’s forerunners. The document, an after-action report for Stratcom’s Global Guardian exercise in 2001, contains summaries about terrorist groups from around the world. Its section on al-Qaeda states: “The group was originally brought together from elements of various insurgent military groups which have fought continuously in the Middle East since the 1980s. Some of these groups had US backing in the past.” Al-Qaeda was formed in 1988 (see August 11-20, 1988) by Arabs who had fought for the US-sponsored mujaheddin in the Soviet-Afghan war (see 1985-1986 and 1986-1992). [US Strategic Command, 12/4/2011]
December 5-17, 2001: Ground Battle for Tora Bora Rages but Is Later Called ‘Grand Charade’
Around December 5, 2001, about three-dozen US special forces position themselves at strategic spots in the Tora Bora region to observe the fighting. Using hand-held laser target designators, they “paint” targets to bomb. Immediately the US bombing becomes more accurate. With this improved system in place, the ground battle for Tora Bora begins in earnest. However, as the Christian Science Monitor later notes, “The battle was joined, but anything approaching a ‘siege’ of Tora Bora never materialized.” No other US troops take part, and US-allied afghans fight unenthusiastically and sometimes even fight for the other side (see Mid-November 2001-Mid-December 2001). [Christian Science Monitor, 3/4/2002] The Tora Bora battle will end with a victory for the US-allied forces by December 17, 2001 (see December 17, 2001). However, the Daily Telegraph will later report, “In retrospect, and with the benefit of dozens of accounts from the participants, the battle for Tora Bora looks more like a grand charade.” Eyewitnesses express shock that the US pinned in Taliban and al-Qaeda forces, thought to contain many high leaders, on three sides only, leaving the route to Pakistan open. An intelligence chief in Afghanistan’s new government says, “The border with Pakistan was the key, but no one paid any attention to it. In addition, there were plenty of landing areas for helicopters had the Americans acted decisively. Al-Qaeda escaped right out from under their feet.” [Daily Telegraph, 2/23/2002]
