The FBI’s New York field office and FBI headquarters in Washington, DC, argue over which of them should lead the bureau’s investigation of the 9/11 attacks and, against precedent, FBI Director Robert Mueller decides to put the headquarters in charge of it.
New York Office Usually Deals with Al-Qaeda Attacks – In the days after the attacks, a major confrontation arises over which facility should be the office of origin for the case. [Graff, 2011, pp. 333-334; Wired, 6/14/2017] The FBI operates under an “office of origin” system, which means that whichever of its 56 field offices opens an official case on a particular subject or group subsequently manages all related matters. The method prevents work being duplicated, and ensures that institutional expertise learned during previous investigations is retained and built on, rather than having to be relearned by a new office when another incident occurs. Under the system, the FBI’s New York office has become the office of origin for al-Qaeda cases and normally deals with al-Qaeda attacks. The office retains most of the bureau’s “institutional knowledge” on Osama bin Laden and al-Qaeda. It led the FBI’s investigations of the bombings of the US embassies in Kenya and Tanzania in August 1998 (see 10:35-10:39 a.m., August 7, 1998), and the attack on the USS Cole in Yemen in October 2000 (see October 12, 2000). [9/11 Commission, 7/24/2004, pp. 74; Soufan, 2011, pp. 82] Mueller, though, wants to run the investigation of the 9/11 attacks from FBI headquarters.
New York Official Objects to Running the Investigation from Washington – He goes to the FBI’s temporary New York field office (see After 10:28 a.m. September 11, 2001) and talks with senior officials there, including Barry Mawn, director of the New York office, Kenneth Maxwell, an assistant special agent in charge at the New York office, and Pasquale D’Amuro, assistant special agent in charge of counterterrorism at the New York office. He explains why he wants FBI headquarters to be the office of origin. Mawn objects, saying the New York office has been the office of origin for the entire al-Qaeda case so far. It has the relevant expertise, investigative capabilities, and files to lead the investigation, he points out, and is also near the Ground Zero crime scene. But Mueller refuses to back down. He says he won’t run the investigation from the headquarters over a conference call. “I want to look someone in the eye,” he comments. [Graff, 2011, pp. 333-334] By October, he will have made the decision to run the investigation from Washington. This is the first time an “operational investigation” has been based at FBI headquarters, according to the Washington Post. [Washington Post, 6/14/2004]
Domestic Terrorism Squad Will Be Assigned to the Case – The case will soon be given the codename PENTTBOM, using the FBI’s standard system for naming cases. This stands for “Pentagon/Twin Towers Bombing.” It is unclear why “BOM” is included in the name, since no bombs were used in the 9/11 attacks. Some agents will later guess that, in the initial confusion, the person who opened the case file incorrectly thought a bomb had been involved. [Graff, 2011, pp. 319-320] D’Amuro will be transferred to Washington and become the leader of the entire case. Instead of being run by one of the FBI’s experienced al-Qaeda squads, I-49 and I-45, a New York domestic terrorism squad called I-44 will be moved to Washington to handle the case. Mary Galligan, who previously spent time as the on-scene commander in the investigation of the attack on the USS Cole, will lead this squad. Some members of the New York Joint Terrorism Task Force will also move to Washington to work on the case.
Former Director Will Disagree with the Decision to Run the Case from Headquarters – Investigators will be based in a large room in the basement of the J. Edgar Hoover Building, where FBI headquarters is located. Two thousand agents will work on the case full-time, following thousands of leads as they pursue information about the attacks. Agents will conduct over 180,000 interviews and review millions of pages of documents. They will log over 155,000 items of evidence and put together a massive timeline, detailing the activities of the alleged 9/11 hijackers in the United States. The investigation will become the largest the FBI has ever conducted. [Washington Post, 6/14/2004; Graff, 2011, pp. 334] However, Louis Freeh, Mueller’s predecessor as FBI director, will criticize Mueller’s decision to run it from FBI headquarters. “I don’t think you can run counterterrorism cases out of headquarters,” he will say. “I think you have to coordinate them out of headquarters,” he will explain, “but you can’t prepare a criminal case for a field presentation in a US district court in headquarters.” [9/11 Commission, 4/13/2004]
Late March through Early June, 2002: FBI Interrogator Gains ‘Actionable Intelligence’ from Zubaida Using Non-Coercive Interrogation Methods
FBI senior interrogator and al-Qaeda expert Ali Soufan, in conjunction with FBI agent Steve Gaudin, interrogate suspected al-Qaeda operative Abu Zubaida (see March 28, 2002) using traditional non-coercive interrogation methods, while Zubaida is under guard in a secret CIA prison in Thailand. A CIA interrogation team is expected but has not yet arrived, so Soufan and Gaudin who have been nursing his wounds are initially leading his questioning using its typical rapport-building techniques. “We kept him alive,” Soufan will later recall. “It wasn’t easy, he couldn’t drink, he had a fever. I was holding ice to his lips.” At the beginning, Zubaida denies even his identity, calling himself “Daoud;” Soufan, who has pored over the FBI’s files on Zubaida, stuns him by calling him “Hani,” the nickname his mother called him. Soufan and Gaudin, with CIA officials present, elicit what he will later call “important actionable intelligence” from Zubaida. To help get him to talk, the agents bring in a box of audiotapes and claim they contain recordings of his phone conversations. He begins to confess.
Zubaida Reveals KSM Is 9/11 Mastermind – Zubaida tells Soufan that Khalid Shaikh Mohammed was the mastermind of the 9/11 attacks, and confirms that Mohammed’s alias is “Mukhtar,” a vital fact US intelligence discovered shortly before 9/11 (see August 28, 2001). Soufan shows Zubaida a sheaf of pictures of terror suspects; Zubaida points at Mohammed’s photo and says, “That’s Mukhtar… the one behind 9/11” (see April 2002). Zubaida also tells Soufan about American al-Qaeda operative Jose Padilla (see March 2002 and Mid-April 2002). In 2009, Soufan will write of his interrogations of Zubaida (see April 22, 2009): “This experience fit what I had found throughout my counterterrorism career: traditional interrogation techniques are successful in identifying operatives, uncovering plots and saving lives.” When the CIA begins subjecting Zubaida to “enhanced interrogation tactics” (see Mid-April 2002), Soufan will note that they learn nothing from using those tactics “that wasn’t, or couldn’t have been, gained from regular tactics. In addition, I saw that using these alternative methods on other terrorists backfired on more than a few occasions… The short sightedness behind the use of these techniques ignored the unreliability of the methods, the nature of the threat, the mentality and modus operandi of the terrorists, and due process.” [Vanity Fair, 7/17/2007; Mayer, 2008, pp. 155; New York Times, 4/22/2009; Newsweek, 4/25/2009]
Standing Up to the CIA – The CIA interrogation team members, which includes several private contractors, want to begin using “harsh interrogation tactics” on Zubaida almost as soon as they arrive. The techniques they have in mind include nakedness, exposure to freezing temperatures, and loud music. Soufan objects. He yells at one contractor (whom other sources will later identify as psychologist James Mitchell—see Late 2001-Mid-March 2002, January 2002 and After and Between Mid-April and Mid-May 2002), telling him that what he is doing is wrong, ineffective, and an offense to American values. “I asked [the contractor] if he’d ever interrogated anyone, and he said no,” Soufan will later say. But, Mitchell retorts that his inexperience does not matter. “Science is science,” he says. “This is a behavioral issue.” Instead, Mitchell says, Soufan is the inexperienced one. As Soufan will later recall, “He told me he’s a psychologist and he knows how the human mind works.” During the interrogation process, Soufan finds a dark wooden “confinement box” that the contractor has built for Zubaida. Soufan will later recall that it looked “like a coffin.” (Other sources later say that Mitchell had the box constructed for a “mock burial.”) An enraged Soufan calls Pasquale D’Amuro, the FBI assistant director for counterterrorism. “I swear to God,” he shouts, “I’m going to arrest these guys!” Soufan challenges one CIA official over the agency’s legal authority to torture Zubaida, saying, “We’re the United States of America, and we don’t do that kind of thing.” But the official counters with the assertion that the agency has received approval from the “highest levels” in Washington to use such techniques. The official even shows Soufan a document that the official claims was approved by White House counsel Alberto Gonzales. It is unclear what document the official is referring to.
Ordered Home – In Washington, D’Amuro is disturbed by Soufan’s reports, and tells FBI director Robert Mueller, “Someday, people are going to be sitting in front of green felt tables having to testify about all of this.” Mueller orders Soufan and then Gaudin to return to the US, and later forbids the FBI from taking part in CIA interrogations (see May 13, 2004). [New York Times, 9/10/2006; Newsweek, 4/25/2009]
Disputed Claims of Effectiveness – The New York Times will later note that officials aligned with the FBI tend to think the FBI’s techniques were effective while officials aligned with the CIA tend to think the CIA’s techniques were more effective. [New York Times, 9/10/2006] In 2007, former CIA officer John Kiriakou will make the opposite claim, that FBI techniques were slow and ineffective and CIA techniques were immediately effective. However, Kiriakou led the team that captured Zubaida in Pakistan and does not appear to have traveled with him to Thailand (see December 10, 2007). [ABC News, 12/10/2007; ABC News, 12/10/2007 
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Press Investigation Finds that FBI Interrogations Effective – In 2007, Vanity Fair will conclude a 10 month investigation comprising 70 interviews, and conclude that the FBI techniques were effective. The writers will later note, “America learned the truth of how 9/11 was organized because a detainee had come to trust his captors after they treated him humanely.” CIA Director George Tenet reportedly is infuriated that the FBI and not the CIA obtained the information and he demands that the CIA team get there immediately. But once the CIA team arrives, they immediately put a stop to the rapport building techniques and instead begin implementing a controversial “psychic demolition” using legally questionable interrogation techniques. Zubaida immediately stops cooperating (see Mid-April 2002). [Vanity Fair, 7/17/2007]
Early August 2002: Wolfowitz Pressures FBI to Confirm That Prague Meeting Took Place
Several Pentagon officials, including Deputy Defense Secretary Paul Wolfowitz, meet with the FBI’s assistant director for counterterrorism, Pat D’Amuro, to discuss the latest intelligence concerning the alleged April 2001 (see April 8, 2001) meeting between 9/11 plotter Mohamed Atta and Iraqi diplomat Ahmed Khalil Ibrahim Samir al-Ani. Wolfowitz pressures the FBI briefers to confirm that the Prague meeting had in fact happened. The FBI concedes that the occurrence of the meeting, though not proven, was at least possible. [Time, 9/2/2002]
January 10, 2003: Government Employees Responsible for 9/11 Failures Are Rewarded and Promoted
FBI Director Robert Mueller personally awards Marion (Spike) Bowman with a presidential citation and cash bonus of approximately 25 percent of his salary. [Salon, 3/3/2003] Bowman, head of the FBI’s national security law unit and the person who refused to seek a special warrant for a search of Zacarias Moussaoui’s belongings before the 9/11 attacks (see August 28, 2001), is among nine recipients of bureau awards for “exceptional performance.” The award comes shortly after a 9/11 Congressional Inquiry report saying Bowman’s unit gave Minneapolis FBI agents “inexcusably confused and inaccurate information” that was “patently false.” [Star-Tribune (Minneapolis), 12/22/2002] Bowman’s unit was also involved in the failure to locate 9/11 hijackers Khalid Almihdhar and Nawaf Alhazmi after their names were put on a watch list (see August 28-29, 2001). In early 2000, the FBI acknowledged serious blunders in surveillance Bowman’s unit conducted during sensitive terrorism and espionage investigations, including agents who illegally videotaped suspects, intercepted e-mails without court permission, and recorded the wrong phone conversations. [Associated Press, 1/10/2003] As Senator Charles Grassley (R-IA) and others have pointed out, not only has no one in government been fired or punished for 9/11, but several others have been promoted: [Salon, 3/3/2003] 
Richard Blee, chief of Alec Station, the CIA’s bin Laden unit, was made chief of the CIA’s new Kabul station in December 2001 (see December 9, 2001), where he aggressively expanded the CIA’s extraordinary rendition program (see Shortly After December 19, 2001). Blee was the government’s main briefer on al-Qaeda threats in the summer of 2001, but failed to mention that one of the 9/11 hijackers was in the US (see August 22-September 10, 2001). In addition to Blee, the CIA also promoted his former director for operations at Alec Station, a woman who took the unit’s number two position. This was despite the fact that the unit failed to put the two suspected terrorists on the watch list (see August 23, 2001). “The leaders were promoted even though some people in the intelligence community and in Congress say the counterterrorism unit they ran bore some responsibility for waiting until August 2001 to put the suspect pair on the interagency watch list.” CIA Director George Tenet has failed to fulfill a promise given to Congress in late 2002 that he would name the CIA officials responsible for 9/11 failures. [New York Times, 5/15/2003] Pasquale D’Amuro, the FBI’s counterterrorism chief in New York City before 9/11, was promoted to the bureau’s top counterterrorism post. [Time, 12/30/2002] FBI Supervisory Special Agent Michael Maltbie, who removed information from the Minnesota FBI’s application to get the search warrant for Moussaoui, was promoted to field supervisor and goes on to head the Joint Terrorism Task Force at the FBI’s Cleveland office. [Salon, 3/3/2003; Newsday, 3/21/2006] David Frasca, head of the FBI’s Radical Fundamentalist Unit, is “still at headquarters,” Grassley notes. [Salon, 3/3/2003] The Phoenix memo, which was addressed to Frasca, was received by his unit and warned that al-Qaeda terrorists could be using flight schools inside the US (see July 10, 2001 and July 27, 2001 and after). Two weeks later Zacarias Moussaoui was arrested while training to fly a 747, but Frasca’s unit was unhelpful when local FBI agents wanted to search his belongings—a step that could have prevented 9/11 (see August 16, 2001 and August 20-September 11, 2001). “The Phoenix memo was buried; the Moussaoui warrant request was denied.” [Time, 5/27/2002] Even after 9/11, Frasca continued to “[throw] up roadblocks” in the Moussaoui case. [New York Times, 5/27/2002] Dina Corsi, an intelligence operations specialist in the FBI’s bin Laden unit in the run-up to 9/11, later became a supervisory intelligence analyst. [US Department of Justice, 11/2004, pp. 279-280 ; CNN, 7/22/2005] Corsi repeatedly hampered the investigation of Almihdhar and Alhazmi in the summer of 2001 (see June 11, 2001, June 12-September 11, 2001, Before August 22, 2001, August 27-28, 2001, August 28, 2001, August 28-29, 2001, and (September 5, 2001)). President Bush later names Barbara Bodine the director of Central Iraq shortly after the US conquest of Iraq. Many in government are upset about the appointment because of her blocking of the USS Cole investigation, which some say could have uncovered the 9/11 plot (see October 14-Late November, 2000). She did not apologize or admit she was wrong. [Washington Times, 4/10/2003] However, she is fired after about a month, apparently for doing a poor job. An FBI official who tolerates penetration of the translation department by Turkish spies and encourages slow translations just after 9/11 was promoted (see March 22, 2002). [CBS News, 10/25/2002]
