While the 9/11 hijackers are in the US, the NSA intercepts several calls between them and an al-Qaeda communications hub in Sana’a, Yemen, run by Ahmed al-Hada, who is hijacker Khalid Almihdhar’s father-in-law (see August 4-25, 1998).
Summary of Calls – 
The first calls are made by Almihdhar and are intercepted during the spring and summer of 2000 (see Spring-Summer 2000). More calls are made by hijacker Nawaf Alhazmi after the bombing of the USS Cole in October 2000 (see Mid-October 2000-Summer 2001). The final call from the US is intercepted just a few weeks before 9/11 (see (August 2001)).
The NSA intercepted the hijackers’ calls outside the US before this (see Early 1999 and December 29, 1999) and continues to do so in 2000 (see Summer 2000) after Almihdhar returns to Yemen (see June 10, 2000 and (Mid-June-Mid-July 2000)).
Calls’ Content – Some of the calls may only contain non-operational information, as they are reportedly between Almihdhar and his wife. [9/11 Commission, 7/24/2004, pp. 222; Suskind, 2006, pp. 94; Wright, 2006, pp. 343] However, the calls are also used to relay messages to the 9/11 hijackers. [Embassy of Yemen (Washington), 2/13/2002; MSNBC, 2/14/2002; MSNBC, 5/2005]
Agencies’ Roles – The CIA is the lead agency monitoring the communications hub. It has planted bugs inside it and is wiretapping all calls (see Late August 1998). Intercepts of calls to and from the hub are a major plank of the US intelligence community’s effort to fight al-Qaeda. Also involved is the FBI, which is using phone records to plot these calls on a map (see Late 1998-Early 2002). Some of the calls intercepted by US intelligence come from Osama bin Laden’s satellite phone in Afghanistan (see August 4-25, 1998 and Late August 1998). After 9/11, counterterrorism officials will say that the number was one of the hottest targets being monitored by the NSA and was an “intelligence bonanza.” [Los Angeles Times, 12/21/2005; Wright, 2006, pp. 343]
Importance of Failure – Also after 9/11, counterterrorism officials will agree that the failure to follow leads to the US from this number was a huge missed opportunity to stop the 9/11 plot. For instance, FBI agent Kenneth Maxwell will say: “Two al-Qaeda guys living in California—are you kidding me? We would have been on them like white on snow: physical surveillance, electronic surveillance, a special unit devoted entirely to them.” [MSNBC, 7/21/2004; New Yorker, 7/10/2006 
]
Discussed after 9/11 – The failure to roll up the plot based on these communications intercepts will be discussed following 9/11 (see Summer 2002-Summer 2004 and March 15, 2004 and After).
Summer 2001: FBI Officials Warn New York Officials about the Possibility of a Major Terrorist Attack Occurring
John O’Neill, special agent in charge of the FBI’s national security division in New York, and two other senior FBI officials meet New York City Mayor Rudolph Giuliani and New York City Police Commissioner Bernard Kerik to discuss the threat of an imminent terrorist attack. O’Neill attends the briefing along with Kenneth Maxwell, the FBI agent in charge of counterterrorism in New York, and Barry Mawn, director of the FBI’s New York office. The three men present evidence indicating an imminent terrorist plot. Maxwell says everything suggests a big attack is being planned. At the end of the briefing, Kerik asks, “Could that happen here?” Maxwell says the attack is more likely to occur abroad than in the United States. “I can’t say for sure that it wouldn’t, but historically al-Qaeda has always attacked us overseas,” he replies. All the same, he adds, “They’re definitely planning something huge.” FBI agents are currently trying to determine what is happening with the summer’s high level of al-Qaeda threats (see Summer 2001). “Things were happening; people were on standby,” FBI agent Abby Perkins will later comment. But, Perkins will say, “Everyone thought it’d be an international attack.” [Graff, 2011, pp. 298]
2:30 p.m. September 11, 2001: New York FBI Agent Recognizes the Name of a Hijacker during a Conference Call with FBI Headquarters
A number of FBI agents in New York are told the names of some suspected hijackers during a conference call with FBI headquarters in Washington, DC, and one of the agents, Steve Bongardt, is enraged when he recognizes one of these men, Khalid Almihdhar, as someone the FBI has been investigating. Most agents from the FBI’s New York office have assembled at a temporary field office at 26th Street and the West Side Highway (see After 10:28 a.m. September 11, 2001). But members of the FBI’s I-49 squad, which is focused on Osama bin Laden and al-Qaeda’s central command, have returned to their office at 290 Broadway. Three of them now participate in a conference call with FBI headquarters. Along with Bongardt, Kenneth Maxwell, the agent in charge of counterterrorism in New York, and John Liguori, a supervisor at the New York office, are on the call. Those at headquarters who are on it include Michael Rolince, head of the FBI’s international terrorism operations section, supervisor Rod Middleton, and analyst Dina Corsi. Maxwell begins the discussion, asking: “What do we know? Do we recognize any of the hijacker names?” Corsi says they have some names of suspected hijackers and starts reading these out. When she mentions Almihdhar, Bongardt interrupts her, asking: “Khalid Almihdhar? The same one you told us about? He’s on the list?” [Graff, 2011, pp. 313; Soufan, 2011, pp. 290-291] “This is the same Almihdhar we’ve been talking about for three months!” he yells angrily. [Washington Post, 9/21/2002] “Steve, we did everything by the book,” Middleton explains. “I hope that makes you feel better; tens of thousands are dead!” Bongardt retorts. Maxwell then tries to calm his colleague down. He presses the mute button on the phone and tells Bongardt: “Now is not the time for this. There will be a time, but not now.” [Graff, 2011, pp. 313; Soufan, 2011, pp. 290-291] Sometime tonight, Bongardt will submit a request to the FBI information center. “Within hours,” he will later recall, the center gets back to him after finding Almihdhar’s address in San Diego, California, simply through searching “public resources.” [US Congress. Senate. Committee on Intelligence, 9/20/2002]
September 12-30, 2001: FBI Headquarters Is Put in Charge of Investigating the 9/11 Attacks, against Usual FBI Practice
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]
