In July 2001, Mohammad Sidique Khan, the lead suicide bomber in the 7/7 London bombings (see July 7, 2005), trains in an al-Qaeda camp in Afghanistan (see July 2001). Presumably later in the year, he is sent on a mission to Southeast Asia, where he meets al-Qaeda leader Hambali. Making a total of two trips to the region, Khan is assigned to assess for al-Qaeda how much funding its Southeast Asian affiliate Jemaah Islamiyah (JI) needs. This is according to a militant who will later be jailed in Malaysia. This militant says he takes Khan to meet Nasir Abbas, a JI leader, who then takes Khan to a JI training camp on the southern Philippine island of Mindanao, where Khan learns bomb-making skills. Abbas will later corroborate the account after being captured in Indonesia. [Time, 9/26/2005; Manila Times, 10/27/2005] Abbas will claim that while Khan is in the Philippines, he meets Azhari Husin, a chief bomb-maker for JI who is linked to most of JI’s major bombings. While Husin is Indonesian, he studied in Reading, England, and received a doctorate in engineering there in 1990. [Evening Standard, 10/26/2005] Abbas, the brother-in-law of Ali Gufron, another JI leader and one of the masterminds of the 2002 Bali bombings, will be captured in April 2003. He will be able to avoid a jail term by fully cooperating with the authorities, but it is unknown if his information about Khan is shared with British intelligence before the 7/7 bombings. [New Straits Times, 4/3/2004]
Late 2001: NSA Domestic Wiretapping Ties Up FBI with Bad Leads
The National Security Agency begins sending data—consisting of telephone numbers, e-mail addresses, and names—to the FBI that was obtained through surveillance of international communications originating within the US (see After September 11, 2001 and October 2001). The NSA sends so much data, in fact, that hundreds of agents are needed to investigate the thousands of tips per month that the data is generating. However, virtually all of this information leads to dead ends and/or innocent people. FBI officials repeatedly complain that the unfiltered information is bogging down the bureau: according to over a dozen current and former law enforcement and counterterrorism officials, the flood of tips provide them and their colleagues with very few real leads against terrorism suspect. Instead, the NSA data diverts agents from more productive work. Some FBI officials view the NSA data as pointless and likely illegal intrusions on citizens’ privacy. Initially, FBI director Robert Mueller asks senior administration officials “whether the program had a proper legal foundation,” but eventually defers to Justice Department legal opinions. One former FBI agent will later recall, “We’d chase a number, find it’s a schoolteacher with no indication they’ve ever been involved in international terrorism—case closed. After you get a thousand numbers and not one is turning up anything, you get some frustration.” A former senior prosecutor will add, “It affected the FBI in the sense that they had to devote so many resources to tracking every single one of these leads, and, in my experience, they were all dry leads. A trained investigator never would have devoted the resources to take those leads to the next level, but after 9/11, you had to.” Former NSA director Bobby Ray Inman says that the problem between the FBI and the NSA may stem in part from their very different approaches. Signals intelligence, the technical term for the NSA’s communications intercepts, rarely produces “the complete information you’re going to get from a document or a witness” in a traditional FBI investigation, he says. And many FBI officials are uncomfortable with the NSA’s domestic operations, since by law the NSA is precluded from operating inside US borders except under very specific circumstances. [New York Times, 1/17/2006]
Late 2001: Israeli Government Reportedly Privately Admits to Running Spy Operation in US Before 9/11
The Forward, a popular Jewish weekly in the US, will later report that at the end of 2001, the Israeli government admits to having conducted a large-scale spying operation in the US before 9/11, using art students and moving vans as cover stories. The Forward quotes an anonymous former US official said to have been regularly briefed about the US investigation into Israeli spying: “The assessment was that Urban Moving Systems was a front for the Mossad and operatives employed by it. The conclusion of the FBI was that they were spying on local Arabs but that they could [be deported] because they did not know anything about 9/11.” He further claims that US officials confront the Israeli government at this time and Israel privately admits the operation while continuing to publicly deny it. Israel privately apologizes for violating a secret gentlemen’s agreement between the two countries under which espionage on each other’s soil is coordinated in advance. The Forward notes, “Most experts and former officials interviewed for this article said that such so-called unilateral or uncoordinated Israeli monitoring of radical Muslims in America would not be surprising.” [Forward, 3/15/2002] In 2007, Mark Perelman, the author of the 2002 Forward story that made these claims, will say he still stands by his story and his sources in the Mossad don’t deny it. CounterPunch also will claim to independently confirm Israel’s admission through two former CIA officers. [CounterPunch, 2/7/2007]
Late 2001: Scientist Linked to Al-Qaeda Interrogated, then Released by Pakistani Authorities; FBI Unable to Extradite Suspect
Abdur Rauf, a Pakistani microbiologist whose letters to Ayman al-Zawahiri were uncovered by coalition forces in Kandahar (see (1999-2001)), is arrested and interrogated by Pakistani police. US officials are initially satisfied by the cooperation they are receiving from Pakistan. Rauf consents to questioning and provides useful information. However, Pakistan resists US efforts to bring criminal charges, including indictment and prosecution in the United States. In 2003, Pakistani authorities will cut off FBI access to Rauf, claiming that there is not enough evidence to charge him. A 2006 report by the Washington Post will find that the scientist has been allowed to return to a normal life and that the FBI investigation is on “inactive status.” [Washington Post, 10/31/2006]
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).
Late 2001-Mid-March 2002: CIA Looks to Brutal Torture Techniques of Egyptians, Saudis, and Soviets in Setting Up Its Interrogation Program
On September 17, 2001, President Bush gave the CIA broad powers to interrogate prisoners (see September 17, 2001), but the CIA does not have many officers trained in interrogation. As a result, in late 2001 and early 2002, while the CIA waits for high-ranking al-Qaeda leaders to be captured, senior CIA officials begin investigating which interrogation procedures to use. [New York Times, 9/10/2006] The CIA “construct[s] its program in a few harried months by consulting Egyptian and Saudi intelligence officials and copying Soviet interrogation methods long used in training American servicemen to withstand capture.” [New York Times, 10/4/2007] Both Egypt and Saudi Arabia are notorious for their brutal and widespread use of torture. The Soviet interrogation techniques mentioned were designed not to get valuable intelligence, but to generate propaganda by getting captured US soldiers to make statements denouncing the US. The CIA hires two psychologists willing to use the techniques, James Elmer Mitchell and Bruce Jessen, even though the two have no never conducted any real world interrogations and there is no evidence at the time (or later) that the Soviet torture techniques are effective in obtaining valuable intelligence and not just false confessions (see Mid-April 2002). [New York Times, 9/10/2006; New York Times, 10/4/2007] In mid-March 2002, the CIA will draw up a list of ten permissible aggressive interrogation techniques based on the advice from these governments and psychologists (see Mid-March 2002).
Late 2001 and After: CNN Limits Critical Reporting of Bush Administration Due to Pressure and Patriotic Fervor
In 2007, Walter Isaacson, chairman and CEO of CNN in the early 2000s, will say: “There was a patriotic fervor and the Administration used it so that if you challenged anything you were made to feel that there was something wrong with that.… And there was even almost a patriotism police which, you know, they’d be up there on the internet sort of picking anything a Christiane Amanpour, or somebody else would say as if it were disloyal… Especially right after 9/11. Especially when the war in Afghanistan is going on. There was a real sense that you don’t get that critical of a government that’s leading us in war time.” When CNN starts showing footage of civilian casualties in Afghanistan, people in the Bush administration and “big people in corporations were calling up and saying, ‘You’re being anti-American here.’” [PBS, 4/25/2007] So in October 2001, Isaacson sends his staff a memo, which says, “It seems perverse to focus too much on the casualties or hardship in Afghanistan.” He orders CNN to balance such coverage with reminders of the 9/11 attacks. [Washington Post, 10/31/2001] Isaacson will add, “[W]e were caught between this patriotic fervor and a competitor [Fox News] who was using that to their advantage; they were pushing the fact that CNN was too liberal that we were sort of vaguely anti-American.” An anonymous CNN reporter will also later say, “Everybody on staff just sort of knew not to push too hard to do stories critical of the Bush Administration.” [PBS, 4/25/2007]
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: US Citizen Captured in Afghanistan, Declared to Be ‘Enemy Combatant’
Yaser Esam Hamdi, who holds dual Saudi and US citizenship, is captured in Afghanistan by the Northern Alliance and handed over to US forces. According to the US government, at the time of his arrest, Hamdi carries a Kalashnikov assault rifle and is traveling with a Taliban military unit. The following month he will be transferred to Guantanamo. In April 2002, it will be discovered he is a US citizen. He will be officially be declared an “enemy combatant” and transferred to a Navy brig in Norfolk, Virginia (see April 2002). [CNN, 10/14/2004]
