Abu Musab al-Zarqawi, a Jordanian-born Palestinian, travels to Afghanistan in 1989 and fights against the pro-Soviet government there. He becomes a radical Islamist and reportedly trains at an al-Qaeda training camp there. He forms a militant group later known as al-Tawhid. In 1993, he returns to Jordan but is quickly arrested for possessing grenades and is sentenced to 15 years in prison. But he gathers many followers inside the prison and is connected to growing Jordanian radical militant networks outside the prison. In May 1999, Abdullah II becomes the new king of Jordan and al-Zarqawi is released from prison as part of a general amnesty. [Atlantic Monthly, 6/8/2006] In late 1999, al-Zarqawi is allegedly involved in an unsuccessful attempt to blow up the Radisson SAS Hotel in Amman, Jordan (see November 30, 1999). [Guardian, 10/9/2002; Independent, 2/6/2003; Washington Post, 2/7/2003] By the end of 1999, he returns to Afghanistan and meets bin Laden. However, bin Laden reportedly strongly dislikes him, because al-Zarqawi comes across as too ambitious, abrasive, and overbearing, and has differing ideological views. But another al-Qaeda laeder, Saif al-Adel, sees potential and convinces bin Laden to give a token $5,000 to set up his own training camp near the town of Herat, close to the border with Iran. He begins setting up the camp in early 2000 (see Early 2000-December 2001). [Atlantic Monthly, 6/8/2006]
Mid-1990s: Hezbollah Allegedly Trains Some Al-Qaeda Operatives in Explosives
In 2001, Jamal al-Fadl, a highly reliable al-Qaeda defector (see June 1996-April 1997), will claim that numerous al-Qaeda operatives went to Lebanon and received training from the militant group Hezbollah. Double agent Ali Mohamed sets up a meeting between Osama bin Laden and Hezbollah leader Imad Mugniyah in early 1994 (see Shortly After February 1994). After that meeting, al-Fadl will claim, the following al-Qaeda figures train with Hezbollah: 
Saif al-Islam al-Masri, a member of al-Qaeda’s military ruling council. Abu Talha al-Sudani, an al-Qaeda leader living in Somalia. Saif al Adel, al-Qaeda’s probable number three leader after the death of Mohammed Atef in 2001. Two others. One of them runs one of al-Qaeda’s training camps in Afghanistan.
Al-Fadl will add that some videotapes are brought back and he sees one of them. It teaches how to blow up “big buildings.” [United States of America v. Usama Bin Laden, et al., Day 2, 2/6/2001] Ali Mohamed will also claim in court that Hezbollah subsequently provides explosives training for al-Qaeda and Islamic Jihad. So will US prosecutor Patrick Fitzgerald, who states, “in the middle of the 1990s, al-Qaeda members received sophisticated explosives training from Hezbollah, despite the deep religious differences between the Sunni members of al-Qaeda and the Shiite members of Hezbollah.” [9/11 Commission, 6/16/2004] However, it seems the links between al-Qaeda and Hezbollah decline after this time.
February 5, 1998: US Rejects Sudanese Al-Qaeda Files that Could Stop Embassy Bombings
Gutbi al-Mahdi, head of Sudan’s intelligence agency, sends a letter to David Williams, an FBI station chief. It reads, “I would like to express my sincere desire to start contacts and cooperation between our service and the FBI. I would like to take this opportunity with pleasure to invite you to visit our country. Otherwise, we could meet somewhere else.” Apparently the FBI is very eager to accept the offer and gain access to Sudan’s files on bin Laden and his associates. The US had been offered the files before (see March 8, 1996-April 1996; April 5, 1997), but the US position was that Sudan’s offers were not serious since Sudanese leader Hassan al-Turabi was ideologically close to bin Laden. But al-Turabi has lost power to moderates by this time, and in fact he is placed under arrest in 1998. There is a political battle between US agencies over the Sudanese offer, and in the end the State Department forbids any contact with al-Mahdi. On June 24, 1998, Williams is obliged to reply, “I am not currently in a position to accept your kind invitation.” Al-Madhi later will complain, “If they had taken up my offer in February 1998, they could have prevented the [US embassy] bombings.” Tim Carney, US ambassador to Sudan until 1997, will say, “The US failed to reciprocate Sudan’s willingness to engage us on serious questions of terrorism. We can speculate that this failure had serious implications – at the least for what happened at the US Embassies in 1998. In any case, the US lost access to a mine of material on bin Laden and his organization.” One of the plotters in the bombings is Fazul Abdullah Mohammed (a.k.a. Haroun Fazul), who is living in Sudan but making trips to Kenya to participate in the bombing preparations. Sudan has files on him and continues to monitor him. Sudan also has files on Saif al-Adel, another embassy bomber who has yet to be captured. Sudan also has files on Wadih El-Hage and Mamdouh Mahmoud Salim, both of whom have contact with members of the Hamburg al-Qaeda cell (see September 16, 1998; Late 1998; 1993). Salim even attends the same small Hamburg mosque as 9/11 hijackers Mohamed Atta and Marwan Alshehhi. Vanity Fair magazine will suggest that if al-Madhi’s offer had been properly followed up, both the embassy bombings and the 9/11 attacks could have been foiled. [Vanity Fair, 1/2002] It is later revealed that the US was wiretapping bin Laden in Sudan on their own (see Early 1990s).
Early 2000-December 2001: Al-Zarqawi Operates Independent Militant Training Camp in Afghanistan
In early 2000, Islamist militant leader Musab Abu al-Zarqawi starts a new training camp in Afghanistan, near the town of Herat. Osama bin Laden reportedly does not like him, but al-Zarqawi gets some help from al-Qaeda leader Saif al-Adel, who serves as a liaison between al-Zarqawi and al-Qaeda. His camp starts with only a dozen or so followers, but it rapidly grows and eventually numbers several thousand. His group consists mostly of Jordanians and Syrians, and is helped by links to the Muslim Brotherhood. According to the Atlantic Monthly, bin Laden repeatedly asks al-Zarqawi to come to him and take an oath of allegiance, but each time al-Zarqawi refuses. “Under no circumstances did [al-Zarqawi] want to become involved in the battle between the Northern Alliance and the Taliban. He also did not believe that either bin Laden or the Taliban was serious enough about jihad.” But in October 2001, the US begins bombing Afghanistan, and al-Zarqawi’s camp is targeted. He is reportedly wounded in the chest when a ceiling falls on him. But in December 2001, he manages to escape to Iran with about 300 followers and is based there for several months while regrouping. [Atlantic Monthly, 6/8/2006]
March-April 2001: Al-Qaeda Defector Describes Plot to Hijack US Airplane
In March 2001, the ISI learns that one of bin Laden’s operatives, who is working on a sensitive al-Qaeda job in Afghanistan, has been providing information to the CIA at the US consulate in Peshawar, Pakistan. The operative, whose CIA codename is “Max,” becomes worried that the ISI will disclose to al-Qaeda his dealings with the CIA. The next month, ABC News reporters Chris Isham and John Miller meet with Max and help him defect to the US and talk to the FBI. Max tells the reporters that in 1999 and 2000 he was trained as part of a small group by Saif al-Adel, one of al-Qaeda’s top leaders. Asked by Isham and Miller whether al-Qaeda is planning any operations targeting the US, he describes a plan to hijack an airplane carrying a US senator or ambassador and then use the dignitary to bargain for the release of the “Blind Sheikh,” Sheikh Omar Abdul-Rahman. US intelligence learned of the same basic plot idea in 1998 (see 1998). Max does defect and will be extensively debriefed by the FBI. [Miller, Stone, and Mitchell, 2002, pp. 282] In May 2001, a Senior Executive Intelligence Brief (SEIB) will be sent to top White House officials warning that “terrorist groups [are] cooperating on [a] US hostage plot”(see May 23, 2001). It is not known for how long Max was talking to the CIA or what he told them before he was exposed, but his account contradicts assertions that US intelligence did not have any well placed informants in al-Qaeda in Afghanistan. An Afghan named “Ahmed” defects around the same time and there are similarities between his case and that of Max, but it is unknown if they are in fact the same person or not (see April 2001).
Summer 2001: Candidate 9/11 Hijacker Possibly Arrested in US, Then Released
A candidate 9/11 hijacker named Abderraouf Jdey is possibly arrested and then released in the US around this time, although details remain very murky.
CIA Officer’s Curious Report – In 2010, Rolf Mowatt-Larssen will write a public report for the Harvard Kennedy School entitled, “Al Qaeda Weapons of Mass Destruction Threat: Hype or Reality?” Mowatt-Larssen was a CIA official from 1982 to 2005, and was head of the CIA’s Counterterrorism Center (CTC) for a time. Around the time of 9/11, he was the head of the CTC’s weapons of mass destruction branch (see 1982, Early October-December 2001, and November 2005). In a timeline in Mowatt-Larssen’s report, there is this entry for Summer 2001: “Detention of Abderraouf Yousef Jdey, a biology major with possible interest in biological and nuclear weapons, who traveled with Zacharias Moussaoui from Canada into the United States. Moussaoui is detained with crop duster manuals in his possession; Jdey had biology textbooks. Earlier, they attended McMaster University in Canada, along with Adnan Shukrijumah.” This entry is very curious, because although the report is said to be based entirely on publicly sourced material, there has been no public information about Jdey’s arrest or link with Moussaoui, and the footnotes to the entry do not mention these things either. [Mowatt-Larson, 1/2010 
]
Jdey’s 9/11 Connection – In late 1999, Jdey may have attended an advanced training course in Afghanistan also attended by 9/11 hijackers Khalid Almihdhar and Nawaf Alhazmi (see Late 1999). He may also have been instructed by 9/11 mastermind Khalid Shaikh Mohammed at the same time as hijacker Mohamed Atta and Ramzi bin-al-Shibh. A letter recovered from a safe house in Afghanistan in late 2001, apparently written by al-Qaeda leader Saif al-Adel, says that Jdey was originally meant to be one of the 9/11 hijackers. A videotape of Jdey pledging to be a martyr was also discovered in mid-November 2001 in Afghanistan, in the wreckage of al-Qaeda leader Mohammed Atef’s house (see November 15-Late December 2001). [9/11 Commission, 7/24/2004, pp. 527]
Jdey Is Highly Wanted After 9/11 – Jdey was born in Tunisia, but became a Canadian citizen in the mid-1990s. After 9/11, it is known that he leaves Canada in November 2001. In January 2002, the US government will announce they are seeking him. In 2005, the FBI will announce a $5 million reward for him. [Los Angeles Times, 1/26/2002; CBC News, 5/27/2004; Rewards for Justice, 4/2005]
Mystery Is Unresolved – If Mowatt-Larssen is correct and Jdey was arrested before 9/11, this would have been a vital opportunity to stop the 9/11 plot, and if he was connected with Moussaoui, that would dramatically change the circumstances of Moussaoui’s arrest. It would also mean there would had to have been a cover-up of Jdey’s arrest in the years since 9/11.
October 10, 2001: FBI Issues List of 22 Most Wanted Terrorists; $5 Million Reward Placed on All of Them
The FBI releases a list of its 22 most wanted terrorists. The US government offers up to $5 million for information leading to the capture of anyone of the list. The men are: Al-Qaeda leaders Osama bin Laden, who was indicted by a grand jury in 1998 (see June 8, 1998), Ayman al-Zawahiri, linked to a 1995 bombing in Pakistan (see November 19, 1995), and Mohammed Atef, who provided training to Somali fighters before the Black Hawk Down incident (see Late 1992-October 1993); Khalid Shaikh Mohammed (KSM), for his role in the 1995 Bojinka plot (see January 6, 1995). KSM is actually the mastermind of 9/11, although the US intelligence community has allegedly not yet pieced this information together (see (November 7, 2001)); Several other operatives suspected of involvement in the 1998 US embassy bombings in Africa (see 10:35-10:39 a.m., August 7, 1998): Fazul Abdullah Mohammed (see August 2, 2008), Mustafa Fadhil, Usama al-Kini (a.k.a. Fahid Muhammad Ally Msalam (see August 6-7, 1998)), Ahmed Khalfan Ghailani (see July 25-29, 2004), Sheikh Ahmed Salim Swedan (see July 11, 2002), Abdullah Ahmed Abdullah (see September 10, 2002), Anas al-Liby (see January 20, 2002- March 20, 2002), Saif al-Adel (see Spring 2002), Ahmed Mohammed Hamed Ali, and Mushin Musa Matwalli Atwah (see April 12, 2006); Abdul Rahman Yasin, a US-Iraqi involved in the 1993 World Trade Center bombing (see March 4-5,1993); Ahmed Ibrahim Al-Mughassil, Ali Saed Bin Ali El-Houri, Ibrahim Salih Mohammed Al-Yacoub, and Abdelkarim Hussein Mohamed Al-Nasser, for their alleged part in the 1996 Khobar Towers bombing in Saudi Arabia (see June 25, 1996); Imad Mugniyah, Hassan Izz-Al-Din, and Ali Atwa for the hijacking of TWA Flight 847 in June 1985. [CNN, 10/10/2001]
Spring 2002: Much of Al-Qaeda’s Management Council Detained in Iran, Held as Bargaining Chips with US
In the spring on 2002, as the Taliban is collapsing in Afghanistan, many al-Qaeda operatives flee into neighboring Iran. About 20 to 25 operatives composing much of al-Qaeda’s management council are said to wind up in the custody of Iran’s Revolutionary Guard. Prior to this point, the Iranian government has been turning over most al-Qaeda captives to other countries, but after President Bush’s “Axis of Evil” speech criticizing Iran (see January 29, 2002), Iran decides to keep this group. [Washington Post, 7/9/2004] Iran does not officially admit to holding them, and their status is unclear, but they all seem to be living in a village near the Caspian Sea. One senior US intelligence official says, “They are under virtual house arrest,” and not able to do much. Those said to be in Iranian custody include: Saif al-Adel, one of al-Qaeda’s top military commanders. Suliman abu Ghaith, al-Qaeda spokesman. Saad and Hamza bin Laden, two of Osama bin Laden’s young sons. Abu Dahak, who served as al-Qaeda’s liaison to the rebels in Chechnya. Mustafa Abu al-Yazid, a financial expert. Two unnamed top aides to Ayman al-Zawahiri. [MSNBC, 6/24/205] Thirwat Salah Shehata, a member of Islamic Jihad’s ruling council, who is probably one of the al-Zawahiri aides mentioned above. [MSNBC, 5/2005] Mustafa Hamza, head of Al-Gama’a al-Islamiyya, an Egyptian militant group, and an al-Qaeda leader as well (see June 26, 1995). In late 2004, he will be extradited from Iran to stand trial in Egypt. [Reuters, 1/9/2005]
At first, these operatives appear to be capable of communicating with operatives outside of Iran. Saad bin Laden is said to play a major role planning the attack of a synagogue in Tunisia in April 2002 (see April 11, 2002). But the Saudi government will suspect that some of the operatives in Iran are involved in a 2003 attack in Riyadh, Saudi Arabia (see May 12, 2003), and they will successfully press Iran to tighten the house arrest of the operatives in Iran. Iran will propose an exchange of these prisoners around the time of the Riyadh bombing, but the US will reject the offer (see Mid-May 2003). Since that time, these leaders apparently remain in a state of limbo. CIA Director Porter Goss will say in 2005, “I think [the] understanding that there is a group of leadership of al-Qaeda under some type of detention—I don’t know exactly what type, necessarily—in Iran is probably accurate.” [MSNBC, 6/24/205] Michael Scheuer, former head of the CIA’s bin Laden unit, will later ask, “The question is, what does house arrest mean in the Iranian context?” He suggests that Iran could release the group or loosen their restrictions depending on how relations evolve between the US and Iran. “They’re a guarantee against bad behavior.” [Washington Post, 9/9/2007] In 2006, it will be reported that Saad bin Laden has been freed. [Reuters, 8/2/2006] Also in 2006, al-Yazid will emerge as a leader of al-Qaeda forces in Afghanistan and may never have been in Iran. [Washington Post, 9/9/2007] In 2007, the still teenaged Hamza bin Laden will reportedly appear in Afghanistan. [Associated Press, 9/11/2007] In 2008, it will be reported that the US still knows little about the al-Qaeda figures detained in Iran, but US officials say they believe Iran has largely kept them under control since 2003, limiting their ability to travel and communicate. One US official will say, “It’s been a status quo that leaves these people, some of whom are quite important, essentially on ice.” [ABC News, 5/29/2008]
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 10-11, 2002: Al-Qaeda Safe Houses Shut Down in Karachi, Pakistan
A suspected al-Qaeda operative named Ahmed Ghulam Rabbani is arrested in a safe house in Karachi, Pakistan, on September 10, 2002. He is a Saudi who later became a Pakistani citizen. Starting in 2000, he began running an al-Qaeda safe house in Karachi. He will be held in Pakistani custody until he is transferred to a US prison in Afghanistan in May 2004. He will be sent to the US-run Guantanamo prison in Cuba in September 2004. His driver, Muhammad Madni, is arrested too, and Madni reportedly quickly reveals the location of other safe houses in Karachi. [US Department of Defense, 5/26/2008] Abdul Rahim Ghulam Rabbani, Ahmed Ghulam Rabbani’s brother, is arrested at one of the safe houses this same day. According to Abdul Rahim’s 2008 Guantanamo file, he is an important al-Qaeda figure because he began running up to six Karachi safe houses, on behalf of 9/11 mastermind Khalid Shaikh Mohammed (KSM), from early 2000 until his capture. According to his file, many important al-Qaeda leaders stayed at his safe houses and interacted with him or his brother while they were passing through Karachi, including: Saif al-Adel, Abd al-Rahim al-Nashiri, Khallad bin Attash, Saad bin Laden, KSM, Ali Abdul Aziz Ali, Musaad Aruchi, and Hassan Ghul (who is said to be his brother-in-law). Furthermore, 17 of the 19 9/11 hijackers stayed at his safe houses while coming or going through Pakistan, including Mohamed Atta, Marwan Alshehhi, Hani Hanjour, and Ahmed Alghamdi (the others are not mentioned in his Guantanamo file by name). Abdul Rahim does not admit knowing their mission, but says he picked them up at airports, kept them at safe houses, and transported some of them to their next destinations. He apparently is working on a plot to bomb Karachi hotels used by Westerners, but it is scuttled by the arrests. He is held by Pakistan for two months, then he will be handed to US forces and held in various prisons in Afghanistan until September 2004, when he is transferred to Guantanamo. [US Department of Defense, 6/9/2008] The next day, these other safe houses are raided by the ISI (Pakistan’s intelligence agency). 9/11 hijacker associate Ramzi bin al-Shibh is arrested at one of the safe houses (see September 11, 2002). However, in contrast to the claim that the arrest of Ahmed Ghulam Rabbani led to the arrest of bin al-Shibh and others, there is a claim that an Al Jazeera reporter, Yosri Fouda, interviewed bin al-Shibh and KSM in a Karachi safe house in the middle of 2002 (see April, June, or August 2002), then told the emir of Qatar, Sheikh Hamad bin Khalifa al-Thani, where the interview took place, and the emir told the CIA. The CIA then began intensely monitoring Karachi for safe houses, which finally led to these raids (see June 14, 2002 and Shortly After). Hassan Ali bin Attash, brother of al-Qaeda leader Khallad bin Attash, is arrested at the same safe house as bin al-Shibh. Hassan will later be named by many other Guantanamo prisoners as an al-Qaeda operative, but not nearly as important a one as his brother. He will later say that he was held by the Pakistani government for a few days, then taken to Kabul, Afghanistan, by US forces for a few days, and then sent to Jordan and kept in Jordanian custody for over a year. He will be transferred to Guantanamo in January 2004, and where he subsequently remains. [US Department of Defense, 6/25/2008] One other suspected al-Qaeda operative is arrested at the safe house with bin al-Shibh and bin Attash (located on Tariq Road). The three of them allegedly hold knives to their throats and threaten to kill themselves rather than be captured. But they are overwhelmed after a four-hour stand-off. [US Department of Defense, 12/8/2006] At another safe house, there is a gun battle when it is raided. Two suspected al-Qaeda operatives are killed. One of those killed, Hamza al-Zubayr, is considered an al-Qaeda leader and the leader of the group in the house. The remaining six are arrested. All six will later be transferred to Guantanamo. [US Department of Defense, 6/25/2008] All of the above is based on Guantanamo files leaked to the public in 2011 by the non-profit whistleblower group WikiLeaks. There are many doubts about the reliability of the information in the files (see April 24, 2011).
