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).
Late 2001: KSM Sheltered by Royal Family Members in Qatar
The New York Times will later report that Khalid Shaikh Mohammed (KSM) hides in Qatar for two weeks with the support of some members of the Qatari royal family. KSM stays there “with the help of prominent patrons” after fleeing from Kuwait. One of the Qatari royals sheltering KSM is possibly Abdul Karim al-Thani, who has repeatedly sheltered Islamist militant leader Abu Musab al-Zarqawi and given passports and more than $1 million to al-Qaeda. It is also possible that KSM may have received help from Abdallah bin Khalid al-Thani, who is Qatar’s Interior Minister by this time and who allowed KSM live on his farm for several years until 1996 (see January-May 1996). CIA Director George Tenet is reportedly infuriated, but no action is taken. In fact, the US military will base its headquarters for the Iraq war in Qatar (see March 28, 2003). [New York Times, 2/6/2003]
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: FBI Links KSM to Financing of 9/11 Attacks
Khalid Shaikh Mohammed (KSM) is allegedly first linked to the 9/11 plot around this time. According to an unnamed US counterterrorism official speaking to a reporter in June 2002 (see June 4, 2002), when KSM is first publicly identified as the 9/11 mastermind, “within three months” of 9/11, the FBI learns that KSM was involved in some financial transactions related to the funding of the 9/11 attacks. [Associated Press, 6/4/2002] KSM is also connected to the 9/11 hijackers in another way in November 2001 (see (November 2001)).
December 19, 2001: Al-Qaeda Operative Sufaat Arrested, May Hold Key to 9/11-Crop Duster Mystery
Yazid Sufaat is arrested in Malaysia. Sufaat is a Malaysian who owns a condominum in Kuala Lumpur, Malaysia, where a January 2000 al-Qaeda summit was held (see January 5-8, 2000). He also graduated in 1987 from a California university with a degree in biological sciences. According to interrogations of Khalid Shaikh Mohammed, Hambali, and other captured prisoners, Sufaat was given the lead in developing chemical and biological weapons for al-Qaeda, but he apparently had been unable to buy the kind of anthrax he wanted for an attack. Zacarias Moussaoui, Mohamed Atta, and other al-Qaeda operatives appeared to have had an interest in crop dusters before 9/11. It has been suggested that this interest served to further Sufaat’s biological weapons plot. This would especially make sense in the case of Moussaoui, since he stayed with Sufaat in Sufaat’s Malaysia apartment for two months in late 2000 (see September-October 2000). The US will only be able to directly interview Sufaat on one brief occasion, in November 2002. [Washington Post, 3/28/2003; CNN, 10/10/2003; Chicago Tribune, 12/7/2003] Sufaat will be released in 2008. The Malaysian government will never try or charge him (see December 4, 2008).
December 22, 2001: Shoe Bomber Plot Foiled, Bomber Claims Allegiance to Bin Laden
British citizen Richard Reid is arrested for trying to blow up a Miami-bound jet using explosives hidden in his shoe. [Associated Press, 8/19/2002] Reid fails in his attempt to destroy the American Airlines jet because he is unable to detonate the explosives—he cannot get the fuse to light using matches, despite using up six of them before he is overpowered by the stewards and passengers. Authors Sean O’Neill and Daniel McGrory will comment, “Had Reid used a cheap disposable plastic cigarette lighter to ignite the fuse of his bomb, rather than a match that did not burn for long enough, forensic experts are sure there was enough plastic explosive in his boot to puncture the fuselage of Flight 63 and bring down the aircraft.” [O’Neill and McGrory, 2006, pp. 215-217, 236] The attack is supposed to be one of two simultaneous attacks, but Reid’s partner, Saajit Badat, backs out shortly before the bombing (see (December 14, 2001)). Reid will later plead guilty to all charges, and declare himself a follower of Osama bin Laden. [CBS News, 10/4/2002] He may have ties to Pakistan. [Washington Post, 3/31/2002] It is later believed that Reid and others in the shoe bomb plot reported directly to 9/11 mastermind Khalid Shaikh Mohammed (KSM). [CNN, 1/30/2003] It has been suggested that KSM has ties to the ISI, and that Reid is a follower of Ali Gilani, a religious leader believed to be working with the ISI (see January 6, 2002).
December 24, 2001-January 23, 2002: Reporter Daniel Pearl Investigates Sensitive Topics in Pakistan
Wall Street Journal reporter Daniel Pearl writes stories about the ISI that will lead to his kidnapping and murder (see January 31, 2002). 
On December 24, 2001, he reports about ties between the ISI and a Pakistani organization, Ummah Tameer-e-Nau, that was working on giving bin Laden nuclear secrets before 9/11 (see 2000 and Mid-August 2001). [Wall Street Journal, 12/24/2001] A few days later, he reports that the ISI-supported militant organization Jaish-e-Mohammed still has its office running and bank accounts working, even though President Pervez Musharraf claims to have banned the group. The Jaish-i-Mohammed is connected to the Al Rashid Trust, one of the first entities whose assets were frozen by the US after 9/11 and through which funding may have passed on its way to the hijackers in the US (see Early August 2001 and September 24, 2001). “If [Pearl] hadn’t been on the ISI’s radarscope before, he was now.” [Wall Street Journal, 12/31/2001; Guardian, 7/16/2002; Vanity Fair, 8/2002] He begins investigating links between shoe bomber Richard Reid and Pakistani militants, and comes across connections to the ISI and a mysterious religious group called Al-Fuqra. [Washington Post, 2/23/2002] He also may be looking into the US training and backing of the ISI. [Gulf News, 3/25/2002] He is writing another story on Dawood Ibrahim, a powerful Islamic militant and gangster protected by the ISI, and other Pakistani organized crime figures. [Newsweek, 2/4/2002; Vanity Fair, 8/2002] Former CIA agent Robert Baer later claims to be working with Pearl on an investigation of 9/11 mastermind Khalid Shaikh Mohammed. [United Press International, 4/9/2004] It is later suggested that Mohammed masterminds both Reid’s shoe bomb attempt and the Pearl kidnapping, and has connections to Pakistani gangsters and the ISI, so some of these explanations could fit together. [Asia Times, 10/30/2002; CNN, 1/30/2003; United Press International, 4/9/2004] Kidnapper Saeed will later say of Pearl, “Because of his hyperactivity he caught our interest.” [News (Islamabad), 2/15/2002] Pearl is kidnapped on January 23, 2002, and his murder is confirmed on February 22, 2002. [CNN, 2/22/2002]
2002: Most Members of Bojinka Front Company Linked to 9/11 Mastermind Remain at Large
In 1994, several key members of the Bojinka plot, which would have killed thousands if successful (see January 6, 1995), formed a front company called Konsonjaya as part of the plot (see June 1994). Konsonjaya was a trading company that ostensibly exported Malaysian palm oil to Afghanistan and also traded in honey from Sudan and Yemen. All these countries have been important nodes in al-Qaeda’s network. The Philippine government was already wiretapping calls to the Konsonjaya offices before the Bojinka plot was foiled (see 1994), and definitively linked the company to the plot by the spring of 1995 (see Spring 1995). As late as 1998, 9/11 mastermind Khalid Shaikh Mohammed was using Konsonjaya as cover in his international travels (see June 1998). By 1999, the FBI had realized the importance of Konsonjaya to the Bojinka plot, and had linked al-Qaeda leader Hambali to it (see May 23, 1999). [Institute of Defense and Strategic Studies, 3/7/2003 
] In February 2002, Rodolfo Mendoza, the former head of Philippine counter-terrorism who led that country’s Bojinka investigation, will say, “According to my analysis, Konsonjaya was the nerve center not only for business but also for operational supervision [of the Bojinka plot].… The most critical question now is, ‘Where are the other former directors of Konsonjaya?’” [Los Angeles Times, 2/7/2002] Konsonjaya’s eight-person board of directors was made up of: Amein Mohammed (Managing Director). His real name is Mohammed Amin al-Ghafari. He appears to have been heavily involved in the Bojinka plot. However, he has intelligence connections in the Philippines and remains the head of another front connected to Bojinka until November 2002. Then he is implicated in an October 2002 bombing and deported (see 1995 and After, February 15, 1999, and October 8-November 8, 2002). His current whereabouts are unknown. Amein Alsanani (also Managing Director). Annamalai N. L. Sundrasan (Secretary). Wali Khan Amin Shah. He is one of the main Bojinka plotters and will later be sentenced to life in prison in the US for his role in that plot (see September 5, 1996). Medhat Abdul Salam Shabana. Company records show Shabana is from Afghanistan. Riduan bin Isumuddin (Hambali). He is arrested in Thailand in 2003 and taken into US custody (see August 12, 2003). He is believed to have roles in the 9/11 attacks, the 2002 Bali bombings, and other attacks. [Los Angeles Times, 2/7/2002; Institute of Defense and Strategic Studies, 3/7/2003 ] Noralwizah Lee Binti Abdullah (Hambali’s wife). She is arrested with Hambali and immediately extradited to Malaysia. Two months later, the Malaysian government will place her in indefinite detention, where she apparently remains. A Malaysian official will say: “She was more than a wife to Hambali. She was a trusted aide who handled funds of the Jemaah Islamiyah [militant group].” [Institute of Defense and Strategic Studies, 3/7/2003 ; Sydney Morning Herald, 8/16/2003; Associated Press, 10/16/2003] Hemeid H. Alghamdi. He is described in company records as a thirty-year-old Saudi from Jeddah. [Los Angeles Times, 2/7/2002; Institute of Defense and Strategic Studies, 3/7/2003 ] Cosain Ramos (a.k.a. Abu Ali) is also connected to Konsonjaya, but apparently he used an alias so it is not clear which name matches his. He will be arrested in the Philippines in 2002 after being linked to the 2000 Christmas Eve bombings in Indonesia (see December 24-30, 2000 and Shortly Before December 24, 2000). But bizarrely, not only is he not charged, but he is given the job of janitor at the Philippines’s highest security prison and then helps a key al-Qaeda leader escape in 2003 (see July 14, 2003).
The Los Angeles Times reports in February 2002 that the whereabouts of most of the Konsonjaya board of directors remains unknown. [Los Angeles Times, 2/7/2002] But strangely, investigators seemingly remain uninterested in investigating Konsonjaya’s links. In October 2002, Sundrasan, the company’s secretary as well as one of the directors, will contact a Malaysian newspaper and tell them some details about the company, including that Amin Shah opened many bank accounts in the company’s name and that the company never really conducted any business. But he will also say that no investigators, journalists, or officials have ever questioned him about the company. [Malay Mail, 10/24/2002]
2002: CIA Decides Ibrahim Saeed Ahmed Fits Profile of Ideal Courier for Bin Laden
In an attempt to find Osama bin Laden’s whereabouts, CIA intelligence analysts construct a composite profile of what an ideal courier for bin Laden would look like. Then they match this with what they know about bin Laden’s couriers. One US official will later say, “It was like doing the profile of a serial killer.” One courier, whose apparent real name is Ibrahim Saeed Ahmed, fits the profile very closely. However, at this time, US intelligence only knows him by his alias, Abu Ahmed al-Kuwaiti (see Early 2002). He is a Pakistani Pashtun, and speaks Pashto. Most Taliban leaders are Pashtun and speak Pashto. He speaks fluent Arabic, since he grew up in the Persian Gulf. This enables him to speak to bin Laden supporters from many countries in the Muslim world. He is a trusted aide of al-Qaeda leaders Khalid Shaikh Mohammed and Abu Faraj al-Libbi. He had been a part of al-Qaeda for many years prior to 9/11. He is adept at the use of computers. He is fiercely loyal to bin Laden. For instance, according to multiple prisoners at Guantanamo, he was last seen next to bin Laden when bin Laden fled the Tora Bora mountains in December 2001.
An unnamed US official will later say that Ahmed emerged as the most ideal courier for bin Laden, and thus, the best way to get to bin Laden. “He fit all the needs. He was high on the short list,” the official will say. As a result, the search for Ahmed is intensified. More prisoners in US custody are asked what they know about him. [MSNBC, 5/4/2011]
January 23, 2002: Reporter Daniel Pearl Is Kidnapped While Investigating the ISI
Wall Street Journal report Daniel Pearl is kidnapped while investigating the ISI’s connection to Islamic militant groups. [Guardian, 1/25/2002; BBC, 7/5/2002] Saeed Sheikh is later convicted as the mastermind of the kidnap, and though it appears he lured Pearl into being kidnapped beginning January 11, the actual kidnapping is perpetrated by others who remain at large. [Vanity Fair, 8/2002; Wall Street Journal, 1/23/2003] The Guardian later suggests that Pearl must have been under ISI surveillance at the time of his kidnapping. “Any western journalist visiting Pakistan is routinely watched and followed. The notion that Daniel Pearl, setting up contacts with extremist groups, was not being carefully monitored by the Secret Services is unbelievable—and nobody in Pakistan believes it.”
[Guardian, 4/5/2002] Both al-Qaeda and the ISI appear to be behind the kidnapping. The overall mastermind behind the kidnapping seems to be Khalid Shaikh Mohammed, also mastermind of the 9/11 attacks. [Time, 1/26/2003; CNN, 1/30/2003]
