Gary Berntsen, leader of the CIA effort in Afghanistan, names the four most wanted terrorist suspects in Afghanistan at a meeting of his team. They are al-Qaeda leader Osama bin Laden, his second in command Ayman al-Zawahiri, al-Qaeda military commander Mohammed Atef, and Khalid Shaikh Mohammed (KSM). Berntsen places one of his subordinates in charge of these four men, giving orders to “find and kill” them. Berntsen also wants the Taliban’s top three intelligence officials killed. [Berntsen and Pezzullo, 2005, pp. 114] While the connections between the other three and al-Qaeda are well known by this time, the US government apparently first develops information indicating KSM is the mastermind behind 9/11 during FBI questioning of military training camp facilitator Abu Zubaida around April 2002. [New York Times, 4/22/2009] However, KSM is an known terrorist and one of the top 22 fugitives named by the FBI the previous month (see October 10, 2001).
November 15, 2001: Al-Qaeda Leader Reported Killed in Bombing Raid
Al-Qaeda leader Mohammed Atef (a.k.a. Abu Hafs) is believed to have been killed in Gardez, near Kabul, Afghanistan. Atef is considered al-Qaeda’s military commander, and one of its top leaders. Initial reports claim he was killed by a US bombing raid, but later reports will reveal he was hit by Hellfire missile fired from a Predator drone. [US Department of State, 11/16/2001; ABC News, 11/17/2001; Newsweek, 11/11/2002] CIA Director George Tenet will later indicate that Atef was “a key player in the 9/11 attacks,” but the exact nature of his role has not been revealed. [Tenet, 2007, pp. 187] Documents and videotapes are discovered by US forces in the rubble after the raid. Details on two upcoming al-Qaeda attacks are discovered. Investigators examining the videotapes find images of about 50 al-Qaeda operatives (see November 15-Late December 2001). [Suskind, 2006, pp. 57]
November 15-Late December 2001: US Finds Key Al-Qaeda Tape, Fails to Pass It On for Over a Month
After killing al-Qaeda military commander Mohammed Atef and other operatives with a Predator drone (see November 15, 2001), US forces search the building where he was killed and find lots of evidence about al-Qaeda members and various plots. One of the pieces of evidence found is a casing video for an attack on US personnel in Singapore, which al-Qaeda and Jemaah Islamiyah (JI) have been plotting for some time (see June 2001). [Suskind, 2006, pp. 56-57] Shortly before dying, Atef instructed JI leader Hambali to conduct the operation fast, because of the US invasion of Afghanistan. [US District Court for the Eastern District of Virginia, Alexandria Division, 3/8/2006; US District Court for the Eastern District of Virginia, Alexandria Division, 3/8/2006] In addition, JI is also plotting a wave of embassy attacks. A senior Western diplomat will later comment: “There was an imminent danger. Their plans could have been operational in a week.” However, many militants are arrested in Southeast Asia in mid-December and the attacks never happen. US officials initially claim that the passage of the video to Singapore helps with the arrests. But Singapore authorities later point out that they did not receive the tape until the end of December and they had already arrested everybody by then based on information they had acquired on their own. They had also found a copy of the video in a suspect’s house in Singapore. [Washington Post, 2/3/2002; Washington Post, 2/3/2002; Dallas Morning News, 3/16/2002]
June 4, 2002: Khalid Shaikh Mohammed Is Publicly Identified as 9/11 Mastermind
Khalid Shaikh Mohammed (KSM) is publicly identified as the “mastermind” behind the 9/11 attacks. He is believed to have arranged the logistics while on the run in Germany, Pakistan, and Afghanistan. In 1996, he had been secretly indicted in the US for his role in Operation Bojinka (see January 6, 1995), and the US began offering a $2 million reward for his capture in 1998 (see January 8, 1998), which increased to $25 million in December 2001. An international warrant for his arrest was issued in November 2000 (see November 17, 2000). [Associated Press, 6/4/2002; New York Times, 6/5/2002] According to the New York Times, “In recent months, American counterintelligence officials have identified a small group of other al-Qaeda lieutenants as the crucial figures behind the Sept. 11 attacks” aside from KSM. They include Mohammed Atef (who is already deceased), Abu Zubaida, and Ayman al-Zawahiri. [New York Times, 6/5/2002] There are conflicting accounts of how much US investigators knew about KSM before 9/11. He is Pakistani, although he was born and raised in Kuwait. [CBS News, 6/5/2002] He is an uncle of Ramzi Yousef, the bomber of the World Trade Center in 1993. [New York Times, 6/5/2002] In April 2002, captured al-Qaeda leader Abu Zubaida confessed that KSM was the 9/11 mastermind (see April 2002). It is not known how much US intelligence knew about KSM’s link to the 9/11 attacks prior that, although at least some was known (see (December 2001)).
September 10, 2002: 10 of Al-Qaeda’s 24 Pre-9/11 Leaders Said to Be Killed or Captured
The New York Times reports that 10 out of the 24 al-Qaeda leaders considered most important by the CIA before 9/11 have been killed or captured. [New York Times, 9/10/2002] The four most important figures considered still at large are: 
Osama bin Laden (Saudi). He will be killed in 2011 (see May 2, 2011). Ayman al-Zawahiri (Egyptian). Khalid Shaikh Mohammed (Kuwaiti/Pakistani). He will be captured in 2003 (see February 29 or March 1, 2003). Saif al-Adel (Egyptian).
Other figures considered still at large are: Abdullah Ahmed Abdullah (Egyptian). Mustafa Muhammad Fadhil (Egyptian). Mushin Musa Matwalli Atwah (Egyptian). He will be killed in 2006 (see April 12, 2006). Usama al-Kini (a.k.a. Fahid Muhammad Ally Msalam) (Kenyan). He will be killed in 2009 (see January 1, 2009). Fazul Abdullah Mohammed (a.k.a. Haroun Fazul) (Comoros Islander). He will be killed in 2011 (see June 10, 2011). Mahfouz Walad Al-Walid (a.k.a. Abu Hafs the Mauritanian) (Mauritanian). Amin ul-Haq (Afghan). Midhat Mursi (Egyptian). He will be killed in 2008 (see July 28, 2008). Anas al-Liby (Libyan). He may have been secretly captured already (see January 20, 2002- March 20, 2002). Suliman abu Ghaith (Kuwaiti). Saad bin Laden (Saudi). He apparently will be killed in 2009 (see July 22, 2009). Mustafa Ahmed al-Hawsawi (Saudi). He will be captured in 2003 (see February 29 or March 1, 2003). [New York Times, 9/10/2002]
The four leaders captured are: Abu Zubaida (Palestinian) (see March 28, 2002). Abdul Rahim al-Sharqawi (Yemeni) (see Late 2001 and February 7, 2002). Ibn al-Shaykh al-Libi (Libyan) (see December 19, 2001). Abu Zubair al-Haili (Saudi) (see June 8, 2002 and After). [New York Times, 9/10/2002]
Five of the six leaders believed killed are: Mohammed Atef (Egyptian) (see November 15, 2001). Abu Jaffa (a.k.a. Abu Jafar al-Jaziri) (Algerian). Abu Salah al-Yemeni (Yemeni). Tariq Anwar al-Sayyid Ahmad (Egyptian). Muhammad Salah (a.k.a. Nasr Fahmi Nasr Hasanayn) (Egyptian). [New York Times, 9/10/2002]
The sixth leader believed killed is not named. One year after 9/11, US intelligence identifies 20 current high-ranking al-Qaeda leaders, though it is not mentioned who the six new leaders are who replaced some of the killed or captured leaders. [New York Times, 9/10/2002] This list of leaders, while instructive, is curiously incomplete because it fails to mention al-Qaeda leaders known as important to US intelligence before 9/11, such as Hambali, Khallad bin Attash, Abd al-Rahim al-Nashiri, Thirwat Salah Shehata, Mustafa Abu al-Yazid, Ahmed Khalfan Ghailani, and Mohammed Jamal Khalifa.
September 7, 2006: Newly Released Footage Shows Bin Laden with Ramzi Bin Al-Shibh in 2001
Al Jazeera television broadcasts previously unseen footage of Osama bin Laden meeting with Ramzi bin al-Shibh, who was a roommate and close associate of some of the 9/11 hijackers. The footage is said to have been released by al-Qaeda’s production company, As-Sahab, in time for the fifth anniversary of the 9/11 attacks. Bin al-Shibh is seen sitting and talking with bin Laden and al-Qaeda military leader Mohammed Atef. Atef was killed in November 2001 (see November 15, 2001), so the footage has to be from before then, but it is unknown if it was filmed before or after 9/11. Bin Laden is also shown strolling through an Afghanistan training camp meeting followers. Al Jazeera says some of these followers include some of the 9/11 hijackers, but their faces are not seen so it is unclear if this is the case. But bin Laden addresses the camera at one point and says of his followers preparing for missions, “I ask you to pray for them and to ask God to make them successful, aim their shots well, set their feet strong, and strengthen their hearts.” The video also includes the last testaments of two of the hijackers, Wail Alshehri and Hamza Alghamdi filmed in Kandahar, Afghanistan in March 2001 (see September 7, 2006 and (December 2000-March 2001)). [Associated Press, 9/7/2006; CNN, 9/8/2006]
