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).
2002-2003: Chertoff Advises CIA Can Use Waterboarding and ‘False Flag’ Trickery on Detainees
The New York Times will later report that in 2002 and 2003, Michael Chertoff repeatedly advises the CIA about legality of some aggressive interrogation procedures. Chertoff is head of the Justice Department’s criminal division at the time, and will later become the homeland security secretary. Chertoff advises that the CIA can use waterboarding. And the Times will claim he approves techniques “that did not involve the infliction of pain, like tricking a subject into believing he was being questioned by a member of a security service from another country.” [New York Times, 1/29/2005] It will later be reported that the CIA tricked al-Qaeda leader Abu Zubaida into believing he was in the custody of the Saudis when in fact several US officials were merely pretending to be Saudis (see Early April 2002). Furthermore, Chertoff seems to have been advising on the legality of techniques used against Zubaida, strengthening allegations that ‘false flag’ trickery was used on him. “In interviews, former senior intelligence officials said CIA lawyers went to extraordinary lengths beginning in March 2002 to get a clear answer from the Justice Department about which interrogation techniques were permissible in questioning Abu Zubaida and other important detainees. ‘Nothing that was done was not explicitly authorized,’ a former senior intelligence said. ‘These guys were extraordinarily careful.’” Chertoff also opposed one technique that “appeared to violate a ban in the law against using a ‘threat of imminent death.’” [New York Times, 1/29/2005] This appears to match claims that the CIA proposed but did not implement a plan to place Zubaida into a coffin to convince him he was about to die (see Between Mid-April and Mid-May 2002).
January-April 2002: FBI Gives Control of Al-Qaeda Prisoners to CIA; Bush Rejects Law Enforcement Approach
In the first months after 9/11, the FBI is generally in charge of captured al-Qaeda detainees and the assumption is that these detainees will be sent to the US for criminal prosecutions. However, beginning in January 2002, this policy begins to change. The highest ranking al-Qaeda detainee in US custody at the time, Ibn al-Shaykh al-Libi, is transfered from FBI to CIA custody and then flown to Egypt to be tortured by the Egyptian government (see January 2002 and After).
]]). Also in January, the CIA, not the FBI, begins secretly flying detainees to the US-controlled prison in Guantanamo, Cuba (see January 14, 2002-2005).
Journalist James Risen will later comment, “By choosing the CIA over the FBI, [President] Bush was rejecting the law enforcement approach to fighting terrorism that had been favored during the Clinton era. Bush had decided that al-Qaeda was a national security threat, not a law enforcement problem, and he did not want al-Qaeda operatives brought back to face trial in the United States, where they would come under the strict rules of the American legal system.” [Risen, 2006, pp. 28] This change of policy culminates in the arrest of Abu Zubaida (see March 28, 2002). The Washington Post will later report, “In March 2002, Abu Zubaida was captured, and the interrogation debate between the CIA and FBI began anew. This time, when FBI Director Robert S. Mueller III decided to withhold FBI involvement, it was a signal that the tug of war was over. ‘Once the CIA was given the green light… they had the lead role,’ said a senior FBI counterterrorism official.” [Washington Post, 6/27/2004] The CIA decides that Guantanamo is too public and involves too many US agencies to hold important al-Qaeda detainees. By the time Zubaida is captured the CIA has already set up a secret prison in Thailand, and Zubaida is flown there just days after his capture (see March 2002). Risen will comment, “The CIA wanted secret locations where it could have complete control over the interrogations and debriefings, free from the prying eyes of the international media, free from monitoring by human rights groups, and most important, far from the jurisdiction of the American legal system.” [Risen, 2006, pp. 29-30]
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-March 28, 2002: Intelligence Leads to Al-Qaeda Leader Abu Zubaida’s Location; Accounts Differ
At some time around February 2002, intelligence leads to the location of Abu Zubaida. He will be captured in Faisalabad, Pakistan, in late March 2002 (see March 28, 2002). However, accounts on what intelligence leads to Zubaida’s location differ greatly:
Call to Yemen? – According to the Associated Press, “Pakistani intelligence officials have said quietly that a mobile phone call Abu Zubaida made to al-Qaeda leaders in Yemen led to his arrest.” [Associated Press, 4/20/2002] This could be a reference to the “Yemen hub,” an important al-Qaeda communication node in Yemen that has long been monitored by US intelligence. The hub is used until the middle of February 2002, when it is raided and shut down (see February 13, 2002).
Bribes Play Key Role? – According to books by Jane Mayer and Ron Suskind, Pakistani intelligence officers in Pakistan’s tribal region notice a caravan of vehicles carrying tall women wearing burqas who turn out to be male Islamist militants in disguise. According to Suskind’s version, the militants are arrested, but refuse to talk. According to Mayer’s version, the caravan is allowed to proceed. However, both authors agree that a bribe to the driver of one of the cars reveals that their destination is Faisalabad, Pakistan. Suskind adds that the driver gives up the name of a contact in Faisalabad, and that contact is found and reveals that Zubaida has arrived in town. US intelligence begins intensively monitoring Faisalabad. Afterwards, Mayer claims that the CIA buys the ISI’s help. A CIA source involved in the situation will later tell Mayer, “We paid $10 million for Abu Zubaida.” [Suskind, 2006, pp. 84; Mayer, 2008] In 2006, Pakistani President Pervez Musharraf will write in a memoir, “Those who habitually accuse us of not doing enough in the war on terror should simply ask the CIA how much prize money it has paid to the Government of Pakistan.” [Musharraf, 2006, pp. 190]
CIA Tracks Zubaida’s Calls? – According to a 2008 New York Times article, in February 2002, the CIA learns that Zubaida is in Lahore or Faisalabad, Pakistani cities about 80 miles apart and with a combined population of over 10 million. The Times does not say how the CIA learns this. The CIA knows Zubaida’s cell phone number, although it is not explained how this was discovered either. (However, it had been reported elsewhere that Zubaida’s number had been monitored since at least 1998 (see October 1998 and After) and was still being monitored after 9/11 (see September 16, 2001 and After) and October 8, 2001).) Specialists use an electronic scanner that can track any operating cell phone and give its approximate location. However, Zubaida only turns his phone on briefly to collect messages, so his location cannot be pinpointed. A talented CIA official named Deuce Martinez gets involved. He posts a large, blank piece of paper on a wall, and writes Zubaida’s phone number in the middle of it. Then he and others add linked phone numbers, using the monitoring capabilities of the NSA and Pakistani intelligence. A map of Zubaida’s contacts grows. Eventually, Martinez and others are able to narrow Zubaida’s location down to 14 addresses in Lahore and Faisalabad, and these places are put under surveillance. Rather than wait any longer for more intelligence, all 14 locations are raided at once in a joint Pakistani-CIA operation on March 28, 2002, and Zubaida is found in one of the Faisalabad addresses. [New York Times, 6/22/2008]
Key Call to Bin Laden or Al-Zawahiri? – Suskind’s book will also give the story of the CIA narrowing down the locations by monitoring local phone calls. He says that teams of CIA and FBI arrive in Faisalabad on March 17 for more intensive monitoring. Then, the key break comes near the end of the month, when two calls from a certain house in Faisalabad are made to phone numbers in Afghanistan that might be linked to Osama bin Laden or al-Qaeda number two leader Ayman al-Zawahiri. By this account, US intelligence already has a good idea which of the 14 locations Zubaida is in, because of those calls. [Suskind, 2006, pp. 87-89]
Explanations May Not Conflict – Note that these explanations do not necessarily conflict. For instance, bribes could have provided the lead that Zubaida was in Faisalabad, and then further CIA monitoring could have narrowed down his location there. Bribes also could have helped insure that Pakistani intelligence did not tip off Zubaida prior to the raid. The calls to Yemen and/or Afghanistan may have played a role along with other intelligence.
March 2002: First Secret CIA Prison Built in Thailand
ABC News will later report that the first CIA secret prison is established in Thailand at this time to house Abu Zubaida, the first important al-Qaeda target who is captured at this time (see March 28, 2002). President Bush had recently authorized the creation of CIA prisons (see After February 7, 2002). After being captured in Pakistan and treated for gunshot wounds, Zubaida is flown to Thailand around the middle of April 2002 and housed in a small warehouse inside a US military base. He is waterboarded and interrogated (Mid-May 2002 and After). Later other secret prisons will open in other countries, such as Poland and Romania. [ABC News, 12/5/2005] This prison in Thailand apparently will close some time in 2003. [Washington Post, 11/2/2005] Some reports place the secret prison at the Voice of America relay station near the north-eastern Thai city of Udon Thani close to the border of Laos, but this is unconfirmed. [Sydney Morning Herald, 11/5/2005]
Before March 28, 2002: ’Vast Majority’ of Al-Qaeda Leader’s Contacts Are Already under Surveillance
When al-Qaeda logistics manager Abu Zubaida is arrested in late March 2002 (see March 28, 2002), his computer is searched. According to the Washington Post: “When agents found Zubaida’s laptop computer, a senior law enforcement source said, they discovered that the vast majority of people he had been communicating with were being monitored under FISA warrants or international spying efforts. ‘Finally, we got some comfort’ that surveillance efforts were working, said a government official familiar with Zubaida’s arrest.” The fact some of his contacts are monitored under FISA warrants indicates that they are in the US, as FISA warrants are only used for US targets (see 1978). The monitoring of Abu Zubaida’s communications began in the mid-1990s, at the latest (see (Mid-1996) and October 1998 and After), and continued after 9/11 (see October 8, 2001). [Washington Post, 2/9/2006] Some will later suggest that Zubaida may have had mental problems (see Shortly After March 28, 2002), but this apparently did not stop him from being a key al-Qaeda contact point. FBI agent Dan Coleman, an expert on al-Qaeda, will later say that the FBI “all knew he was crazy, and they knew he was always on the damn phone.” [Washington Post, 12/18/2007] Vincent Cannistraro, former head of the CIA’s Counter Terrorism Center, says of Zubaida shortly after Zubaida’s capture, “He was the guy that had the direct contact with prominent al-Qaeda cell leaders abroad, and he knew where they all were. He would have been the guy co-ordinating new attacks.” [Observer, 4/7/2002]
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]
March 28, 2002-Mid-2004: High-Ranking Al-Qaeda Detainees Subjected to Aggressive Interrogation Techniques
In 2007, NBC News will report that the CIA uses aggressive interrogation techniques on at least 13 high-ranking al-Qaeda detainees between 2002 and 2004. These techniques are first used on Abu Zubaida, captured in March 2002 (see March 28, 2002), and some of the techniques are discontinued in the wake of the Abu Ghraib scandal around the middle of 2004 (see April 28, 2004), which is also around the time the CIA’s Inspector General issues a secret report suggesting many of these techniques could be a violation of an international treaty against torture (see May 7, 2004). Euphemistically called “enhanced interrogation,” these techniques include: 
Sleep deprivation. Exposure to extreme heat and cold. Confined quarters. Psychological and physical abuse. The use of psychotropic drugs. Waterboarding. However, waterboarding is allegedly only used on about four of the detainees (see May 2002-2003).
All 13 of these detainees will later be transferred to Guantanamo prison to stand trial before a military tribunal there (see September 2-3, 2006). (Two others similarly transferred – Abu Faraj al-Libbi and Abd al-Hadi al-Iraqi – are captured after the Abu Ghraib scandal and thus are not subjected to as many interrogation techniques.) [MSNBC, 9/13/2007] However, there are other “ghost detainees” not officially acknowledged as captured by the US government (see June 7, 2007). Some, like Hassan Ghul, Abdul Rahim al-Sharqawi, and Mohammed Omar Abdul-Rahman, are held in the same secret prison as most of the “official” high-ranking detainees later transferred to Guantanamo, so it would seem likely that aggressive techniques have been used on many of them as well. In 2007, President Bush will sign an executive order allowing the CIA to use most of these aggressive techniques again (see July 2007).
