The “Blind Sheikh,” Sheikh Omar Abdul-Rahman, is arrested in Brooklyn after a long stand off. The “Landmarks” plot was rolled up on June 24, 1993, and many of Abdul-Rahman’s close associates were arrested on that day (see June 24, 1993). But Abdul-Rahman moved to the Abu Bakr mosque and stayed there. His presence in a mosque and the many supporters that gathered to surround it makes his arrest difficult. But after long negotiations, on July 3, 1993, he is arrested on immigration charges and taken to prison. [New York Times, 7/3/1993] He will later be charged with a role in the “Landmarks” plot and eventually sentenced to life in prison. [New York Times, 1/18/1996]
December 16, 1994-May 1995: Osama’s Brother-in-Law Khalifa Is Arrested in US
Mohammed Jamal Khalifa, a brother-in-law to bin Laden, is arrested in the US. He is held for visa fraud, but he is believed to be a major terrorist. His arrest takes place at a Holiday Inn in Morgan Hill, California. [San Francisco Chronicle, 10/24/2001] That is only about 20 miles from Santa Clara, where double agent Ali Mohamed is running an al-Qaeda cell (see 1987-1998). Counterterrorism expert Steven Emerson will later say of Khalifa and Mohamed, “It seems to me that they were probably in contact. I’m basing that only intuitively on the fact that they were in the same area, they were close to bin Laden, and they would’ve had an incentive to stay together.” [Lance, 2006, pp. 167] According to one account, Khalifa is arrested on behalf of the government of Jordan, because he is on trial there. [San Francisco Chronicle, 10/24/2001] Another account claims that Philippine authorities “tipped off Federal authorities on Khalifa’s movements.” [Filipino Reporter, 4/27/1995] He is traveling on a Saudi passport. He’d flown into the US from London on December 1 and has papers indicating he would be heading back to the Philippines. [Lance, 2006, pp. 158-159] It has been claimed that the CIA helped him get his US visa (see December 1, 1994). There are many reasons for US authorities to suspect Khalifa is a major terrorist figure: 
He is arrested with Mohammed Loay Bayazid, one of the dozen or so original members of al-Qaeda. Bayazid had attempted to purchase nuclear material for bin Laden the year before (see December 16, 1994). Philippine investigators had recently completed a secret report on terrorist funding. The report focuses on Khalifa, and says his activities in the Philippines strongly link with Muslim extremist movements in Iraq, Jordan, Turkey, Russia, Malaysia, the United Arab Emirates, Romania, Lebanon, Syria, Pakistan, Albania, the Netherlands, and Morocco. It calls a charity which Khalifa runs a “pipeline through which funding for the local extremists is being coursed.” Perhaps not coincidentally, the report was released just one day before Khalifa’s arrest in the US (see December 15, 1994). His possessions, which are quickly examined and translated, include a handwritten manual in Arabic detailing how to set up a terrorist curriculum at a school in the Philippines, giving lessons in bomb-making and assassination. [San Francisco Chronicle, 10/24/2001] Khalifa’s business card was discovered in a search of the New York City residence of Sheikh Omar Abdul-Rahman in 1993 (see August 1993). He is an unindicted coconspirator in the “Landmarks” bombings plot, which would have killed thousands in New York City. The trial is getting underway at this time. Abdul-Rahman will be convicted and sentenced to over 300 years in prison (see June 24, 1993). A State Department cable from days after his arrest states Khalifa is a “known financier of terrorist operations and an officer of an Islamic NGO in the Philippines that is a known Hamas front.” An alias is found in his personal organizer that was also used in a bomb-making manual brought into the US by Ahmad Ajaj, Ramzi Yousef’s travel partner, when the two of them came to the US to implement the 1993 World Trade Center bombing (see September 1, 1992). Bojinka plotter Wali Khan Amin Shah’s phone number is found in Khalifa’s possessions. The Bojinka plot, if successful, also would have killed thousands (see January 6, 1995). [Lance, 2006, pp. 158-159] A number in Pakistan that Ramzi Yousef had used to call the Philippines is found as well. Author Peter Lance will later note that such numbers “should have led the FBI directly to Ramzi Yousef, the world’s most wanted man” at the time. [Lance, 2006, pp. 160]
However, despite this wealth of highly incriminating material, within weeks of his arrest the US will decide to deport him to Jordan (see January 5, 1995). Over the next four months, even more of his links to terrorist activity will be discovered (see Late December 1994-April 1995). But Khalifa will be deported anyway (see April 26-May 3, 1995), and then soon freed in Jordan (see July 19, 1995).
January 6, 1995: Pope Assassination and Bojinka Plot to Bomb Dozen Airplanes Is Foiled
Responding to an apartment fire, Philippine investigators uncover an al-Qaeda plot to assassinate the Pope that is scheduled to take place when he visits the Philippines one week later. While investigating that scheme, they also uncover Operation Bojinka, planned by the same people: 1993 WTC bomber Ramzi Yousef and 9/11 mastermind Khalid Shaikh Mohammed (KSM). [Independent, 6/6/2002; Los Angeles Times, 6/24/2002; Los Angeles Times, 9/1/2002] Many initial reports after 9/11 will claim the fire was accidental and the police discovery of it was a lucky break, but in 2002 the Los Angeles Times will report that the police started the fire on purpose as an excuse to look around the apartment. In the course of investigating the fire, one of the main plotters, Abdul Hakim Murad, is arrested. [Los Angeles Times, 9/1/2002] The plot has two main components. On January 12, Pope John Paul II is scheduled to visit Manila and stay for five days. A series of bombs along his parade route would be detonated by remote control, killing thousands, including the Pope. Yousef’s apartment is only 500 feet from the residence where the Pope will be staying. [Reeve, 1999, pp. 78; Lance, 2006, pp. 138] Then, starting January 21, a series of bombs would be placed on airplanes. [Insight, 5/27/2002] Five men, Yousef, Wali Khan Amin Shah, Abdul Hakim Murad, Abd al-Karim Yousef (a.k.a., Adel Anon, Yousef’s twin brother), and Khalid Al-Shaikh (thought to be an alias for KSM) would depart to different Asian cities and place a timed bomb on board during the first leg of passenger planes traveling to Los Angeles, San Francisco, Honolulu, and New York. They would then transfer to another flight and place a second bomb on board that flight. In all, 11 to 12 planes would blow up in a two day period over the Pacific. If successful, some 4,000 people would have been killed. [Agence France-Presse, 12/8/2001; Insight, 5/27/2002; Contemporary Southeast Asia, 12/1/2002] According to another account, some of the bombs would be timed to go off weeks or even months later. Presumably worldwide air travel could be interrupted for months. [Lance, 2003, pp. 260-61] A second wave of attacks involving crashing airplanes into buildings in the US would go forward later, once the pilots are trained for it (see February-Early May 1995).
January 7-11, 1995: ’Intelligence Gold Mine’ Only Leads to Two More Arrests
After a late night raid of the Manila, Philippines, apartment central to the Bojinka plot (see January 6, 1995), investigators find what the Los Angeles Times will call “an intelligence gold mine.” [Los Angeles Times, 9/1/2002] Very quickly, a team of US intelligence agents joins Philippine investigators to sort through the evidence, which fills three police vans. Investigators are able to match fingerprints in the apartment with fingerprints on record for Ramzi Yousef, already believed to be the mastermind behind the 1993 World Trade Center bombing (see February 26, 1993). There are priests’ robes, pipe bombs, a dozen passports, chemicals, maps of the Pope’s planned route through Manila, and more. [Washington Post, 9/30/2001; Los Angeles Times, 9/1/2002] “The most damning information was gleaned from Yousef’s notebook computer, and four accompanying diskettes.” The data is encrypted and in Arabic, but technicians are quickly able to decipher and translate it. [Washington Post, 9/30/2001] Computer data includes “the names of dozens of associates, and photos of some; a record of five-star hotels; and dealings with a trading corporation in London, a meat market owner in Malaysia, and an Islamic center in Tucson, Ariz.… They describe how money moved through an Abu Dhabi banking firm.” [Washington Post, 9/23/2001] Photographs of all five operatives who would place bombs on airplanes are recovered from a deleted computer file. [Los Angeles Times, 5/28/1995] Wali Khan Amin Shah is identified from one of these five photos, plus a list of cell phone numbers found on the hard drive. He is traced to another Manila apartment and arrested on January 11. Under interrogation, Shah, who soon escapes from custody in unexplained circumstances (see January 13, 1995), confesses that most of the funds for the Bojinka plot were channeled to Yousef through a bank account belonging to Ahmad al-Hamwi, a Syrian working at the International Relations and Information Center (IRIC), a charity front run by Mohammed Jamal Khalifa, Osama bin Laden’s brother-in-law. [Washington Post, 9/30/2001] But despite these leads, Ramzi Yousef is the only other person successfully arrested based on all this data (and Yousef’s arrest will largely be due to an informant responding to an existing tip off program (see February 7, 1995)). The Philippine government will arrest other Bojinka plotters later in the year, including another one of the five operatives assigned to place bombs on the planes, but they will all be released (see April 1, 1995-Early 1996). Al-Hamwi is never arrested, while Khalifa is actually in US custody at the time of the Bojinka raid but is soon let go (see April 26-May 3, 1995). The IRIC will be closed down, but its operations are immediately taken over by another close associate of Khalifa (see 1995 and After).
February 7, 1995: Ramzi Yousef Is Arrested in Pakistan
Ramzi Yousef is arrested in Pakistan, in a safe house owned by Osama bin Laden (see February 1992-February 7, 1995). At the time, Yousef’s uncle Khalid Shaikh Mohammed is staying in the same building and brazenly gives an interview to Time magazine as “Khalid Sheikh,” describing Yousef’s capture. [Lance, 2003, pp. 328] Yousef had recruited Istaique Parker to implement a limited version of Operation Bojinka, but Parker got cold feet and instead turned in Yousef (see February 3-7, 1995). [Lance, 2003, pp. 284-85] Robert I. Friedman, writing for New York magazine, will later report that at this time the CIA “fought with the FBI over arresting Yousef in Pakistan—the CIA reportedly wanted to continue tracking him—and President Clinton was forced to intervene.” [New York Magazine, 3/17/1995] Yousef is rendered to the US the next day and makes a partial confession while flying there (see February 8, 1995).
September 13, 1995: Muslim Militant Rendered by CIA in Croatia, Then Killed in Egypt
Talaat Fouad Qassem, 38, a known leader of the Al-Gama’a al-Islamiyya (the Islamic Group), an Egyptian extremist organization, is arrested and detained in Croatia as he travels to Bosnia from Denmark, where he has been been living after being granted political asylum. He is suspected of clandestine support of terrorist operations, including the 1993 World Trade Center bombing (see February 26, 1993). He also allegedly led mujaheddin efforts in Bosnia since 1990 (see 1990). In a joint operation, he is arrested by Croatian intelligence agents and handed over to the CIA. Qassem is then interrogated by US officials aboard a US ship off the Croatian coast in the Adriatic Sea and sent to Egypt, which has a rendition agreement with the US (see Summer 1995). An Egyptian military tribunal has already sentenced him to death in absentia, and he is executed soon after he arrives. [Associated Press, 10/31/1995; Washington Post, 3/11/2002, pp. A01; Mahle, 2005, pp. 204-205; New Yorker, 2/8/2005] According to the 1999 book Dollars for Terror, two weeks before his abduction, Qassem was in Switzerland negotiating against Muslim Brotherhood leaders. Some Muslim Brotherhood exiles were negotiating with the Egyptian government to be allowed to return to Egypt if they agreed not to use Muslim Brotherhood Swiss bank accounts to fund Egyptian militant groups like Al-Gama’a al-Islamiyya, but Qassem and other radicals oppose this deal. So the removal of Qassem helps the Muslim Brotherhood in their conflict with more militant groups. [Labeviere, 1999, pp. 70-71]
May 21, 1996: Boat Accident Helps Alert CIA to Al-Qaeda Cell in Kenya
A passenger ferry capsizes on Lake Victoria in East Africa and one of the more than 800 who drown is Abu Ubaidah al-Banshiri, al-Qaeda’s military commander (his job will be taken over by Mohammed Atef). Al-Qaeda operatives Wadih El-Hage and Fazul Abdullah Mohammed (a.k.a. Haroun Fazul) show up at the disaster scene to find out if al-Banshiri is still alive. There are many journalists covering the disaster and a Western investigator recognizes Fazul and El-Hage when they happen to appear in some of the widely broadcast footage. [Washington Post, 11/23/1998] El-Hage sends a computer file about the drowning to double agent Ali Mohamed in California. Mohamed’s computer hard drive will be copied by US intelligence in 1997 (see October 1997-September 10, 1998). The CIA already has much of El-Hage’s biography on file by this time. It appears this event, along with the defection of Jamal al-Fadl (see June 1996-April 1997), only strengthen knowledge of the Kenya cell gained earlier in the year (see April 1996). By August 1996, if not earlier, the phones of El-Hage and Fazul in Nairobi are bugged and closely monitored by the CIA and NSA. Apparently, not much is learned from these phone calls because the callers speak in code, but the CIA does learn about other al-Qaeda operatives from the numbers and locations that are being called. This information is shared with the FBI’s Joint Terrorism Task Force (JTTF), and the JTTF becomes “convinced that flipping El-Hage [is] the best way to get to bin Laden.” [Miller, Stone, and Mitchell, 2002, pp. 200]
June 1996-April 1997: Highly Trusted Informant Exposes Al-Qaeda Secrets to US
Jamal al-Fadl, an al-Qaeda operative from al-Qaeda’s first meeting in the late 1980s until 1995, tells the US everything he knows about al-Qaeda. Before al-Fadl’s debriefings, US intelligence had amassed thick files on bin Laden and his associates and contacts. However, they had had no idea how the many pieces fit together. But an official says. “After al-Fadl, everything fell into place.” [Miller, Stone, and Mitchell, 2002, pp. 154-65] The New Yorker will later call al-Fadl “arguably the United States’ most valuable informant on al-Qaeda.” FBI agent Dan Coleman will later say on al-Fadl, “He’s been very, very important to us. When it comes to understanding al-Qaeda, he’s the Rosetta Stone.” FBI agent Mike Anticev will similarly say, “He spoke to us in great detail, and everything that he told us panned out.” CIA officials debrief al-Fadl for a month and a half. Then the CIA hands him, and transcripts of all their interviews with him, over to the FBI. [New Yorker, 9/11/2006] Coleman and US prosecutor Patrick Fitzgerald interrogate al-Fadl at a US military base in Germany for months. [Lance, 2006, pp. 261] Roughly between November 1996 and April 1997, al-Fadl tells the FBI about: The historical background of al-Qaeda. Al-Fadl was one of al-Qaeda’s founding members (see August 11-20, 1988). The structure of al-Qaeda and its leadership composition. Al-Qaeda’s objectives and direction. Its financial infrastructure and networks. Al-Fadl has extensive knowledge of this because he worked as an al-Qaeda financial officer (see December 1996-January 1997). Its connections and collaboration with other terrorist groups and supporters. Its activities against US soldiers in Somalia (see October 3-4, 1993). Its activities in Bosnia. Al-Fadl was sent there on several missions (see Autumn 1992 and Autumn 1992). The Al-Kifah Refugee Center, al-Qaeda’s most important charity front in the US. Al-Fadl worked there in the 1980s (see 1986-1993). Bin Laden’s efforts to acquire weapons of mass destruction. Al-Fadl was personally involved in an effort to buy uranium for al-Qaeda (see Late 1993). [9/11 Commission, 7/24/2004, pp. 479] Bin Laden’s plans to attack either inside the US or US embassies (see Late 1996).
Al-Fadl continues to help US intelligence until current day. For instance, in 2000, he will help US officials capture his brother-in-law, Mohammed Suliman al-Nalfi, who is said to be close to Ayman al-Zawahiri. Al-Nalfi will eventually be sentenced to ten years in prison in the US. Al-Fadl will have no knowledge of the 9/11 plot, but he will continue to identify captured al-Qaeda operatives after 9/11. [New Yorker, 9/11/2006] Interestingly, al-Fadl, a Sudanese citizen, will later claim that he worked with the Sudanese intelligence agency with the direct approval of bin Laden. [Day 2. United States of America v. Usama bin Laden, et al., 2/6/2001]
Late August 1998: CIA Apparently Arrests Top Militant Leaders by Accident
In mid-August 1998, the Mossad intercepts a phone call indicating that an Egyptian militant named Ihab Saqr is planning to meet an Iranian intelligence agent in a hotel in Baku, Azerbaijan, in one week’s time. Saqr is believed to be Ayman al-Zawahiri’s chief of staff. The Mossad is very interested in the Iranian connection but they have no presence in Azerbaijan, so they contact the CIA. The CIA leads a capture operation, with one Mossad agent, Michael Ross, also in attendance. The CIA captures Saqr and two men he is meeting with, but neither of them turn out to be Iranian. The other men are Essam Marzouk and Ahmad Salama Mabruk. Marzouk is an al-Qaeda explosives expert who has just trained the men who bombed two US embassies in Africa earlier in the month. He had been living in Canada and Canadian intelligence has long been suspicious about his militant ties. Mabruk is a known member of Islamic Jihad’s ruling council. The US quickly renditions Saqr, Marzouk, and Mabruk to Egypt. Marzouk is sentenced to 15 years in prison, Mabruk is sentenced to life in prison, and Saqr’s fate in Egypt is unknown. [National Post, 10/15/2005; Ross and Kay, 2007, pp. 214-224] The US discovers a treasure trove of information about al-Qaeda and Islamic Jihad in Mabruk’s laptop (see Late August 1998). But it is unclear why the US was seemingly in the dark and only arresting these figures by chance, because US intelligence had long been monitoring calls between Osama bin Laden and Mabruk in Baku (see November 1996-Late August 1998). Furthermore, Canadian intelligence had also monitored many calls between Mabruk and an Islamic Jihad operative in Canada. (Note that some accounts place the timing of this capture in July 1998, but Canadian intelligence is monitoring Mabruk’s communications up through and after the embassy bombings in August (see August 5-7, 1998 and August 8, 1998 and Shortly After).)
September 10, 1998: Ali Mohamed Secretly Arrested Despite Failure to Share Information Between US Agencies
Ali Mohamed is finally arrested after testifying at a grand jury hearing. The arrest is officially kept secret, but the media will report it one month later. [New York Times, 10/30/1998] Patrick Fitzgerald is on the prosecutor team that subpoenaed Mohamed to appear, but apparently he and the other prosecutors know very little about Mohamed. Fitzgerald blames this on a legal “wall” between intelligence gathering and criminal prosecution. He later will relate what happened on the day Mohamed testified: “Ali Mohamed lied in that grand jury proceeding and left the courthouse to go to his hotel, followed by FBI agents, but not under arrest. He had imminent plans to fly to Egypt. It was believed [by the prosecutors] at the time that Mohamed lied and that he was involved with the al-Qaeda network but Mohamed had not by then been tied to the [embassy] bombings. The decision had to be made at that moment whether to charge Mohamed with false statements. If not, Mohamed would leave the country. That difficult decision had to be made without knowing or reviewing the intelligence information on the other side of the ‘wall.’ It was ultimately decided to arrest Mohamed that night in his hotel room [and he was arrested]. [The prosecution] team got lucky but we never should have had to rely on luck. The prosecution team later obtained access to the intelligence information, including documents obtained from an earlier search of Mohamed’s home by the intelligence team on the other side of ‘the wall.’ Those documents included direct written communications with al-Qaeda members and a library of al-Qaeda training materials that would have made the decision far less difficult. (We could only obtain that access after the arrest with the specific permission of the Attorney General of the United States, based upon the fact that we had obligations to provide the defendant with discovery materials and because the intelligence investigation of Mohamed had effectively ended.)… Mohamed [later] stated that had he not been arrested on that day in September 1998, he had intended to travel to Afghanistan to rejoin Osama bin Laden. Thus, while the right decision to arrest was made partly in the dark, the ‘wall’ could easily have caused a different decision that September evening that would have allowed a key player in the al-Qaeda network to escape justice for the embassy bombing in Kenya and rejoin Osama bin Laden in a cave in Afghanistan, instead of going to federal prison.” [US Congress, 10/21/2003] Mohamed’s associate Khaled Abu el-Dahab, now living in Egypt, wil hear of Mohamed’s arrest and attempt to leave the country, but will be arrested in October 1998. He will be put on trial there and sentenced to 15 years in prison (see 1999). [San Francisco Chronicle, 11/21/2001]
