According the 9/11 Congressional Inquiry, shortly after the bombing of the US embassy in Nairobi, Kenya (see 10:35-10:39 a.m., August 7, 1998), a foreign government sends the CIA a list of individuals who flew into Nairobi before the attack. The CIA recognizes that one of the names is an alias for Khalid Shaikh Mohammed (KSM). The report that identified this alias also describes KSM as being close to bin Laden. [US Congress, 7/24/2003] Yet the 9/11 Commission will fail to mention KSM’s role in the embassy bombings and instead will suggest that KSM is not yet a member of al-Qaeda at this time and only joined al-Qaeda after being impressed by the results of the embassy bombings. [9/11 Commission, 7/24/2004, pp. 149-150]
September 1998-January 1999: US Fails to Capture KSM Again as He Makes Second Attempt to Assassinate Pope
9/11 mastermind Khalid Shaikh Mohammed (KSM) lived in the Philippines for much of 1994 and took part in the failed Bojinka plot to assassinate Pope John Paul II and crash a dozen airplanes (see January 6, 1995). In the years after this, he makes repeated visits to the Philippines, as well as neighboring Malaysia. [Los Angeles Times, 9/1/2002] KSM returns to the Philippines in September 1998 and stays to organize the assassination of Pope John Paul II, who is due to visit the country in January 1999. KSM is seen at a nightclub in Manila in early 1999. [Gunaratna, 2003, pp. xxv] But the Pope’s visit is canceled; it isn’t known if the cancellation is due to security concerns or not. That same year, the FBI alerts Philippine intelligence that KSM has returned to that country to visit an old girlfriend. However, he disappears before agents arrive to arrest him. Further details on how he was traced there or how he got away have not been made public. [Los Angeles Times, 9/1/2002; London Times, 11/10/2002] KSM will continue to return to the Philippines occasionally. There are even “credible reports” that he is seen there in the summer of 2002. [Los Angeles Times, 9/1/2002; Knight Ridder, 9/9/2002]
November 1, 1998-February 2001: 9/11 Hijacker Atta and Associates Are Monitored Some by US and Germany in Their Hamburg Apartment
Future 9/11 hijacker Mohamed Atta, al-Qaeda operatives Said Bahaji and Ramzi Bin al-Shibh, and others in the al-Qaeda Hamburg cell move into a four bedroom apartment at 54 Marienstrasse, in Hamburg, Germany, and some of them stay there until February 2001. Investigators will later believe this move marks the formation of the Hamburg al-Qaeda cell. [Los Angeles Times, 1/27/2002; New York Times, 9/10/2002] Up to six men at a time live at the apartment, including, at times, 9/11 hijacker Marwan Alshehhi and cell member Zakariya Essabar. Alshehhi moves out after the first month; it is unclear why. [New York Times, 9/15/2001] During the 28 months Atta’s name is on the apartment lease, 29 Middle Eastern or North African men register the apartment as their home address.
Surveillance of Bahaji – From the very beginning, the apartment is under surveillance by German intelligence, because of investigations into businessman Mamoun Darkazanli that connect to Bahaji. [Washington Post, 10/23/2001] The Germans also suspect connections between Bahaji and al-Qaeda operative Mohammed Haydar Zammar. [Los Angeles Times, 9/1/2002] Bahaji is directly monitored for at least part of 1998, but German officials will not disclose when the probe began or ends. This investigation is dropped for lack of evidence (see (Late 1998)). [Associated Press, 6/22/2002; Los Angeles Times, 9/1/2002] Bahaji moves out in July 1999 and gets married a few months later (see October 9, 1999). [Der Spiegel (Hamburg), 8/29/2011]
Surveillance of El Motassadeq – German intelligence monitors the apartment off and on for months, and wiretaps Mounir El Motassadeq, an associate of the apartment-mates who will later be convicted for assisting the 9/11 plot, but apparently it does not find any indication of suspicious activity (see August 29, 1998). [Chicago Tribune, 9/5/2002]
Surveillance of Zammar – Zammar, a talkative man who has trouble keeping secrets, does not live at the apartment, but he is a frequent visitor to the many late night meetings there. [Miller, Stone, and Mitchell, 2002, pp. 259-60; Los Angeles Times, 9/1/2002; Chicago Tribune, 9/5/2002] He even lives in the apartment for a time in February 1999 (see February 1999). Zammar is the focus of an investigation that began in 1997 and continues until early 2000 (see March 1997-Early 2000). Interest in monitoring him increases in late 1998 (see October 2, 1998).
Surveillance of Atta – The CIA also allegedly starts monitoring Atta in early 2000 while he is living at the apartment, and does not tell Germany of the surveillance (see January-May 2000). Atta leaves Germany to live in the US in June 2000 (see June 3, 2000).
No Direct German Surveillance of the Apartment? – Yet, even though people like Zammar who frequently phone and visit the apartment are monitored, German officials will later claim that the apartment itself is never bugged. An unnamed senior German security official will later say that some surveillance of associated people gives “the impression that the people living there were fanatical believers. At the BfV [Germany’s domestic intelligence agency], we had to decide whether to ask permission to place a wiretap on the line at 54 Marienstrasse itself. We discussed this every day.” But he will claim that they ultimately decide they will not be able to get legal permission for a wiretap because there is no evidence that the apartment’s occupants are breaking any laws. [Vanity Fair, 11/2004] This claim that the apartment was not directly monitored seems contradicted by reports that Bahaji was the target of a surveillance investigation when he was living in the Marienstrasse apartment in late 1998 (see (Late 1998)).
What Would More Surveillance Have Uncovered? – It will later be clear that investigators could have found evidence if they looked more thoroughly. For instance, one visitor will recall Atta and others discussing attacking the US. [Knight Ridder, 9/9/2002] 9/11 mastermind Khalid Shaikh Mohammed is in Hamburg several times in 1999 and comes to the apartment. However, although there is a $2 million reward for Mohammed since 1998, the US apparently fails to tell Germany what it knows about him (see 1999). [Newsweek, 9/4/2002; New York Times, 11/4/2002] 9/11 Hijacker Waleed Alshehri also apparently stays at the apartment “at times.” [Washington Post, 9/14/2001; Washington Post, 9/16/2001] Remarkably, shortly after 9/11, the German government will claim it knew little about the Hamburg al-Qaeda cell before 9/11, and nothing directed it towards the Marienstrasse apartment. [Daily Telegraph, 11/24/2001]
1999: KSM Repeatedly Visits 9/11 Hijacker Atta and Others in Al-Qaeda’s Hamburg Cell
9/11 mastermind Khalid Shaikh Mohammed (KSM) “repeatedly” visits 9/11 hijacker Mohamed Atta and others in the Hamburg al-Qaeda cell. [Associated Press, 8/24/2002] US and German officials say a number of sources place KSM at Atta’s Hamburg apartment, although when he visits, or who he visits while he is there, is unclear. [Los Angeles Times, 6/6/2002; New York Times, 11/4/2002] However, it would be logical to conclude that he visits Atta’s housemate Ramzi Bin al-Shibh, since investigators believe he is the “key contact between the pilots” and KSM. [Los Angeles Times, 1/27/2003] KSM is living elsewhere in Germany at the time. [New York Times, 9/22/2002] German intelligence monitors the apartment in 1999 but apparently does not notice KSM. US investigators have been searching for Mohammed since 1996, but apparently never tell the Germans what they know about him. [New York Times, 11/4/2002] Even after 9/11, German investigators will complain that US investigators do not tell them what they know about KSM living in Germany until they read it in the newspapers in June 2002. [New York Times, 6/11/2002]
Early 1999: KSM Allegedly Works on 9/11 Plot in Hamburg
Counterterrorism expert Rohan Gunaratna will later claim that 9/11 mastermind Khalid Shaikh Mohammed (KSM) visits Hamburg at this time and meets with 9/11 hijacker Mohamed Atta and hijacker associate Ramzi bin al-Shibh. Together, they make plans to carry out the 9/11 attacks in the US. [Gunaratna, 2003, pp. xxx] Other accounts claim KSM repeatedly visits Hamburg this year but do not definitively state who he meets (see 1999). The 9/11 Commission will later claim that the Hamburg al-Qaeda cell including Atta and bin al-Shibh will not be asked to join the 9/11 attacks until late 1999 in Afghanistan (see Between January and October 1999).
1999-September 10, 2001: Some 9/11 Hijackers Possibly Spend Time in Philippines
The names of four hijackers are later discovered in Philippines immigration records. However, whether these are the hijackers or just other Saudis with the same names has not been confirmed. 
Abdulaziz Alomari visits the Philippines once in 2000, then again in February 2001, leaving on February 12. [Associated Press, 9/19/2001; Philippines Inquirer, 9/19/2001; Daily Telegraph, 9/20/2001] Ahmed Alghamdi visits Manila, Philippines, more than 13 times, starting in 1999. He leaves the Philippines the day before the attacks. [Daily Telegraph, 9/20/2001; Arizona Daily Star, 9/28/2001; Filipino Reporter, 10/11/2001] Fayez Ahmed Banihammad visits the Philippines on October 17-19, 2000. [Daily Telegraph, 9/20/2001; Arizona Daily Star, 9/28/2001] Saeed Alghamdi visits the Philippines on at least 15 occasions in 2001, entering as a tourist. The last visit ends on August 6, 2001. [Daily Telegraph, 9/20/2001]
Hijackers Mohamed Atta and Marwan Alshehhi were seen Philippines several times, the last time in December 1999 (see December 1999). 9/11 mastermind Khalid Shaikh Mohammed occasionally stays there as well (see September 1998-January 1999). Nothing more has been heard to confirm or deny the hijackers’ Philippines connections since these reports.
July 8, 1999: FBI Told KSM Is Living in United Arab Emirates
In 2008, the website Intelwire.com will obtain a declassified FBI document from this date. The content is heavily redacted, including the title, but the full title appears to be, “Summary of information obtained from the United Arab Emirates with regard to Manila Air fugitive Khalid Shaikh Mohammed.” The document appears to detail a briefing by United Arab Emirates (UAE) officials from the General Department of State Security to FBI officials visiting the UAE. It mentions that Khalid Shaikh Mohammed (KSM) “who was reported to be in _____ during mid-1998, is still currently living in Sharjah, UAE, with his family.” The report also mentions that “in July 1998, authorities from ______ based on information probably obtained from Qatar, located KSM living and working in ____. After questioning him about his activities with the [Muslim Brotherhood], he was deported to Bahrain.” [Federal Bureau of Investigation, 7/8/1999 
] The 9/11 Commission will later mention this document a single time, and reveal that one of the redacted sections discusses KSM’s links to the Abu Sayyaf militant group in the Philippines. [9/11 Commission, 7/24/2004, pp. 488] Sharjah is a major hub of al-Qaeda activity at this time (see Mid-1996-October 2001), and one of the 9/11 hijackers, Fayez Ahmed Banihammad, is from the emirate of Sharjah (see 1980s and 1990s). 9/11 plot facilitator Mustafa Ahmed al-Hawsawi will be based in Sharjah in the months before the 9/11 attacks, and some of the 9/11 hijackers will pass through there and visit him (see Early-Late June, 2001). It is not known what action US intelligence takes in response to this briefing.
Late 1999: 9/11 Hijackers Train withColeBomber and Other Militants
A group of al-Qaeda operatives receives advanced training at the Mes Aynak camp in Afghanistan. The large group includes 9/11 hijackers Nawaf Alhazmi and Khalid Almihdhar (see November/December 1999), al-Qaeda commander Khallad bin Attash, would-be 9/11 hijacker Abu Bara al-Taizi (a.k.a. Zohair Mohammed Said), USS Cole bomber Ibrahim al-Thawar (a.k.a. Nibras), an operative who leads a series of suicide bombings in Riyadh in 2003, and another who is involved against the 2002 attack against a ship called the Limburg (see October 6, 2002). According to statements by detainees, the course focuses on physical fitness, firearms, close quarters combat, shooting from a motorcycle, and night operations. Osama bin Laden and Khalid Shaikh Mohammed (KSM) apparently visit the camp during the course. [9/11 Commission, 7/24/2004, pp. 157; Office of the Director of National Intelligence, 9/6/2006, pp. 12 ] Candidate hijacker Abderraouf Jdey, a Canadian passport holder, may also be present at this training course. [9/11 Commission, 7/24/2004, pp. 527] Also, in early December, KSM gives special hijacking training to Alhazmi, bin Attash, and al-Taizi (see Early December 1999).
December 1999: 9/11 Hijackers Atta and Alshehhi Seen Partying and Taking Flying Lessons in Philippines
9/11 hijackers Mohamed Atta and Marwan Alshehhi are seen again in the Philippines, partying and taking flying lessons. They stay at the Woodland Park Resort Hotel about sixty miles north of Manila, as they did in 1997 and earlier in 1999. Gina Marcelo, a waitress at the hotel, will later recall that Marwan Alshehhi threw a party there. “There were about seven people. They rented the open area by the swimming pool… They drank Johnnie Walker Black Label whiskey and mineral water. They barbecued shrimp and onions. They came in big vehicles, and they had a lot of money. They all had girlfriends.” [International Herald Tribune, 10/5/2001] 9/11 mastermind Khalid Shaikh Mohammed is also known to be in the Philippines for much of 1999, plotting again to assassinate the Pope (see 1999-September 10, 2001). There are no eyewitness accounts of him being seen with Atta or Alshehhi at this time, but when he lived in the Philippines in 1994 he was known to party and have local girlfriends (see Early 1994-January 1995). Security guard Ferdinand Abad later recalls Mohamed Atta registered under his own name at the hotel this month. Atta went to the nearby Angeles City Flying Club about two of three times a week to train on ultralight aircraft. Abad recalls seeing the flying club van pick up Atta at least five times. Just as when Atta and Alshehhi were at the resort earlier in the year, no one recalls Alshehhi taking flying lessons, only Atta. [Philippine Star, 10/1/2001; Gulf News, 10/2/2001; International Herald Tribune, 10/5/2001] The Philippine military will later confirm that Atta and Alshehhi were at the hotel after finding a number of employees who claim to have seen them. [Philippine Star, 10/1/2001; Gulf News, 10/2/2001] A leader of a militant group connected to al-Qaeda will later confess to helping 9/11 hijacker pilots while they were in this area (see Shortly After October 5, 2005). The 9/11 Commission will not mention the possibility of Atta and Alshehhi staying in the Philippines. They will note that the two of them left Germany in the last week of November 1999 with the intention of going to Afghanistan, but there is no mention of when they arrived in Afghanistan. [9/11 Commission, 7/24/2004, pp. 166-167]
Early December 1999: KSM Trains Operatives for Hijackings
Khalid Shaikh Mohammed (KSM) gives a course lasting one or two weeks for three operatives scheduled to take part in the 9/11 operation. Nawaf Alhazmi, Khallad bin Attash, and Abu Bara al-Taizi (a.k.a. Zohair Mohammed Said) learn how to say basic English words and phrases, read plane timetables and phone books, use the Internet, make travel reservations, rent an apartment, and use code words. In addition, they play flight simulator games, watch hijacking-themed films, and investigate visas for Southeast Asian countries. KSM also tells them what to watch for when casing a flight, for example whether flight attendants bring food into the cockpit. Khalid Almihdhar is apparently not present at the training, since he has just returned to Yemen (see November/December 1999). [9/11 Commission, 7/24/2004, pp. 157-8, 493]
