The CIA’s history with terrorists is a long, complex and horrible tale and no individual story embodies this better than that of Ali Mohamed. Ali was an Egyptian army officer who joined Ayman Al Zawahiri’s Egyptian Islamic Jihad (EIJ) in the early 1980s, and became Al Qaeda’s principal trainer for the first decade of their existence (1988-1998). Meanwhile, he worked as an undercover agent for the CIA, served in the US Special Forces and was an informant for the FBI. How he evaded capture for so long, as well as where he is now, is something of a mystery. He pleaded guilty to numerous terror charges in late 2000 but was never publicly sentenced and there is no record of whether he is in prison or in witness protection or elsewhere. According to his wife he has ‘vanished into thin air’.

Ali was born in Egypt in 1952 and grew up in a middle class family, joining the army in the 1970s and rising to the rank of Major in military intelligence. In 1981 Egyptian President Anwar Sadat was assassinated by members of Ali’s army unit who were also members of EIJ. A fatwa approving the assassination had been issued by The Blind Sheikh Omar Abdel Rahman, the leader of the Egyptian Islamic Group. However, at the time Ali was in the US on an officer exchange training program at Fort Bragg in North Carolina, so he had little if anything to do with the assassination.

Following Sadat’s death there was a crackdown on radical Muslims in Egypt, leading to the imprisonment of Zawahiri and Rahman and in 1984 Ali was expelled from the army for being a fundamentalist. Zawahiri and Rahman ultimately evaded long prison sentences and made their way to Afghanistan to get involved in the jihad against the Soviets. After being rejected by the army Ali worked for a period in the security department for an Egyptian Airline. He then offered his services to the CIA in Cairo.

Ali and the CIA

According to the story now told by the CIA, this was the first and only time Ali worked for them. He was sent undercover to infiltrate a mosque in Hamburg that was affiliated with Hezbollah. Ali reportedly did this successfully within a matter of days, but playing the ‘dangled mole’ strategy he told his targets that he was working for the CIA. Word of this got back to the Agency, who claim they then fired Ali and placed him on the terror watchlist.

However, there are numerous reasons to doubt this story. The first is that by Ali’s own confession he was first approached by the CIA in 1981, during the officer exchange exercise at Fort Bragg. This is what Ali told Dan Coleman, an FBI agent seconded to the CIA’s Bin Laden unit who interrogated (or debriefed) Ali dozens of times after his arrest in 1998. This information was contained in a document from the most official of sources – the Combating Terrorism Center at West Point who produced a profile of Ali in 2007. That profile is no longer on their website, but a backup is here. Coleman also wrote the affidavit that forms the criminal complaint against Ali.

The second reason to think Ali was working for the CIA for a lot longer is that despite being put on the terrorism watchlist following the Hamburg episode, he immediately traveled to the US on a CIA-arranged visa. In September 1985 he flew into New York, meeting a woman called Linda Sanchez on the plane, who he would marry only weeks later. He applied for citizenship and a year after his arrival even joined the US Army, all while he was still on the terror watchlist and making frequent trips to Asia to get involved with EIJ activities.

He was accepted by the army and posted to Fort Bragg, where the US army trains its Special Forces, an extremely unlikely destination for a suspected terrorist. There he was granted the rank of supply sergeant but in reality he was much more. Ali effectively trained US Special Forces in understanding the Islamic world, and Islamic radicalism, at a time when the US was using those very tools to fight the Soviets in Afghanistan. Ali even presented an in-house talk show where he discussed these issues.

Ali clearly wanted to get more involved in the Afghan jihad because in 1988 he took a month’s leave, telling his superiors he was going to Paris. He returned weeks later admitting that he had gone to Afghanistan to fight the Soviets, and even presented to his commanding officer a belt he said he had taken from one of a pair of Spetnaz (Russian Special Forces) soldiers that he had killed. This offence – a US soldier taking it on himself to go off and fight in a war – should have been grounds for court martial, but nothing happened. Likewise, a CIA officer posted at Fort Bragg met with Ali during his time there and even joked afterwards that Ali was probably already a ‘spook’.

Indeed, the whole Fort Bragg chapter of Ali’s story appears to be an extension of his work for the CIA. How else could he have been posted there? Why else would he have been forgiven for disobeying orders and joining a foreign war? His commanding officer, Colonel Robert Anderson, drew attention to this saying, ‘I think you or I would have a better chance of winning Powerball, than an Egyptian major in the unit that assassinated Sadat would have getting a visa, getting to California … getting into the Army and getting assigned to a Special Forces unit.’ He added, ‘That just doesn’t happen’ and explained that he assumed Ali’s place at Fort Bragg was ‘sponsored’ by an intelligence agency, ‘I assumed the CIA.’ Meanwhile, Ali’s friends in California thought he was working as a CIA liaison with the Afghan mujahideen. We have no reason to doubt these opinions and every reason to suspect they are accurate, but the trail gets even thicker.

Ali in NY

Ali finished his stint in the army in 1989 but remained in the Reserve for another five years after that. Meanwhile, in the late 1980s he got involved with a radical mosque in New York at the Al Kifah refugee centre. The mosque had become an important hub for the Maktab al-Khidamat (MAK) or Services Office for the Mujahideen. Through this mosque flowed American Muslim recruits who could be radicalised and sent out to fight in the war against the Godless Commies. Meanwhile, Ali was acting as a translator and fixer for Ayman Zawahiri who was touring the US giving speeches and raising funds for the MAK – the nascent Al Qaeda organisation.

In April and May 1989, only months after Al Qaeda was formally founded in Afghanistan, US officials met with followers of the Blind Sheikh in Cairo. Embassy cables recorded these meetings, and a year later Rahman moved to NY permanently on a CIA-sponsored visa. He and his circle took over the Al Farooq mosque and six months later one of his followers assassinated Rabbi Meir Kahane – a fundamentalist who founded the Jewish Defence League. His killer was El Sayyid Nosair, a man who was inspired by Rahman and trained by Ali Mohamed. The investigation did not sprawl into what was going on at the Al Farooq, and though the Blind Sheik was out of the country at the time and the State Department revoked his visas, he returned to the States a week later and continued to live there for years.

Ali’s trainees also blew up the World Trade Center, bombing it in February 1993. It is even thought that he trained the man who built the bomb – Ramzi Yousef, in Afghanistan in summer 1992. Ali also trained the men who were arrested and convicted for the ‘Day of Terror plot’, a follow-up plot to the WTC bombing by more of the Blind Sheikh’s circle who were provoked and entrapped by FBI informant Emad Salem. While even the Blind Sheikh himself was arrested, prosecuted and convicted, Ali remained free. He even found time to train Bin Laden’s bodyguards in Sudan while all the drama was going on in NY.

In 1994 Mohammed Atef, a major figure in the now fully-functioning Al Qaeda organisation, accused Ali of working for the US government, and refused to tell Ali his real name and his travel plans. In response, Ali obtained a copy of a DOJ list of unindicted co-conspirators in the ‘Day of Terror’ investigation that had his name on it, and presented this as proof of his loyalty to Al Qaeda. However, when defence investigators working for the accused in the Rahman trial tried to find Ali and put him on the witness stand, they couldn’t. Court documents show that the prosecution knew where Ali was, and suggest that DOJ prosecutor Patrick Fitzgerald told Ali to ignore the witness subpoena. Ali never turned up at the trial, and continued to roam free.

Ali in Africa

The African continent also saw the impact of Ali Mohamed’s work. In 1993 he trained Bin Laden’s disciples including the Libyan – Anas Al Liby. Ali and Al Liby toured Africa doing surveillance on possible targets, including the US embassy in Nairobi. According to Ali’s confession it was Bin Laden himself who used Ali’s photo to point to where a truck bomb could be used to attack the embassy.

Al Liby went on to become Al Qaeda’s computer expert and also joined the LIFG, the Libyan Islamic Fighting Group. In the mid 1990s they teamed up with MI6 in an attempt to assassinate then Libyan leader Colonel Gaddafi. The attempt failed and Al Liby and other LIFG members fled to London. They lived in the UK, publishing their newsletter quite openly, until 2000 when a series of raids saw some of their number arrested. Al Liby slipped away, but not without leaving a tell tale sign of his time with Ali – a copy of the Al Qaeda training manual Ali had written.

The manual is a fascinating document and a likely smoking gun for the entire Al Qaeda operation. It was largely compiled by Ali, based on training manuals he had stolen from Fort Bragg in the late 1980s. Some of these manuals turned up in the flat of El Sayyid Nosair, the killer of Meir Kahane, in late 1990. However, the FBI and police investigation did not sprawl into how this ‘lone nut’ shooter obtained classified US Special Forces documents.

Other passages in the manual are eerily reminiscent of the manuals used by the CIA and Pentagon in covert terrorist operations in Latin America, most infamously at their terrorist training centre The School of the Americas. These manuals were in use in the same period – the late 1980s and early 1990s – that Ali wrote the Al Qaeda manual, suggesting that he was tasked to produce the Arabic equivalent of The School of Americas training documents. Even more spooky is the fact that the Latin American manuals were not made publicly available until 1996, meaning Ali must have obtained them via some other route (mostly likely the CIA) in order to be able to translate passages into Arabic several years earlier.

Some years later, in August 1998, the second major Al Qaeda attack on Western targets took place. The embassy bombing attack floated by Ali Mohamed and based on his and Al Liby’s surveillance in 1993 was realised, alongside a twin bombing in Tanzania. Once again Ali had trained the bombers, and had set up and run the cell in Kenya including their front companies, all while operating under the pseudonym ‘Jeff’. Just like the 1993 WTC bombing, the 1998 bombings probably would not have taken place without Ali’s involvement.

Ali’s interrogation

About a month after the dual US embassy bombings, Ali was finally arrested. 17 years after the initial approach from the CIA, a decade after he was serving the US Special Forces, and following several years as a sporadic FBI informant, this ‘terrorist’ was brought to ground. He was then interrogated for two years, primarily by Jack Cloonan and Dan Coleman of the FBI. Both of these men were working inter-agency with the CIA’s Bin Laden unit, and pumped Ali for information on the emerging Al Qaeda threat. Or at least, that’s the official story.

Author and investigative journalist Peter Lance interviewed both Cloonan and Coleman for his book Triple Cross, and according to the version presented by Lance Ali employed delaying tactics for months and months before starting to slowly give up his story. Of course, Lance’s version is largely based on taking official sources at their word and portraying government agencies as overgrown bunglers rather than criminal conspirators. One CIA document suggests otherwise.

In April 1999 the CIA sent a secret intelligence report to the White House, Secretary of State, FBI, ONI, Secret Service and several other agencies containing, ‘not finally evaluated intelligence’ about a ‘targeting study of US Embassy, Nairobi, Kenya’. Even when this report was released in 2012 it was almost entirely redacted, despite being shared in early 1999 with numerous US government departments.

However, what we can establish is that the date being talked about – December 1993 – and the nature of the ‘targeting study’ being reported are entirely consistent with Ali Mohamed’s trip and surveillance operation of the Nairobi embassy. Thus, Ali must have been the source of the ‘not finally evaluated intelligence’ in this report, meaning he was sharing incredibly detailed information about his precise and central role in the embassy bombings plot within about six months of being arrested. This leaves very little time for him to have led Coleman and Cloonan on a merry dance before fessing up, as Peter Lance maintains.

The document in question was released as part of a batch of CIA files used by the 9/11 Commission and referenced in their report. They can be downloaded via Intelwire, who filed the FOIA request and obtained the files. The CIA report is pages 302-312 in binder 2.

Ali and 9/11

Ali was barely referenced at all by the 9/11 Commission. Even though he was a co-operating key intelligence source who had trained Al Qaeda members in hijacking methods they didn’t even ask to speak to him. They did request the FBI’s A-File on Ali Mohamed, but only as one entry in a wide ranging request for documents from the Bureau. They also read books such as The Age of Sacred Terror that detailed significant parts of Ali’s career. One set of notes shows how they knew Ali was the trainer of El Sayyid Nosair and a ‘sergeant in US Special Ops’.

Mysteriously, they never put it together. Or perhaps it isn’t so mysterious. The team in question, team 8 of the 9/11 Commission, were tasked with looking into counter-terrorism policy before 9/11. The man in charge of the team was Michael Hurley, a career CIA officer still employed by the Agency at the time. Perhaps most tellingly, Hurley had served the CIA in Kosovo and Bosnia in the 1990s, when NATO was using Al Qaeda to destabilise the former Yugoslavia and create a civil war that would demand intervention. Some reports even have Ali Mohamed training Al Qaeda in Bosnia, so perhaps we should not raise our eyebrows at Hurley failing to research Ali properly in his role working for the most important investigation in US history.

The other half of this story is that Ali was interrogated by the FBI immediately after 9/11. According to an interview with Cloonan conducted by National Geographic for their show Triple Cross, Ali was one of several prisoners put on lockdown as soon as 9/11 happened, and then asked about it within days. Cloonan said, ‘I don’t believe he was privy to all the details, but what he laid out was the attack as if he knew every detail. This is how you position yourself. I taught people to sit in first class.’ The documentary also claimed that ‘Mohamed described teaching al Qaeda terrorists how to smuggle box cutters onto airplanes’.

The problem with these two details – the hijackers sitting in first class and them using box cutter knives as weapons – is that they have little connection with the real attacks. The FBI/DOJ’s own seating plans for the hijacked planes entered as evidence in the Moussaoui trial, only has some of the hijackers sitting in first class. Mohammed Atta, the supposed ringleader of the entire plot, was apparently content to sit in business class. On Flight 77, which supposedly hit the Pentagon, two of the ‘muscle hijackers’ Majed Moqed and Khalid Al Mihdhar were sat in economy class in seats by the window. This makes no sense if the aim is to quickly and effectively seize control of the aircraft.

Likewise, the evidence that the hijackers used box cutters is sourced from Barbara Olsen, the wife of then Solicitor General Ted Olsen, who apparently died on flight 77. Ted Olsen reports receiving two calls from his wife, but the FBI 302s of their interviews with Olsen himself, members of his office, an AT&T operator and the exhibit from the Moussaoui trial all contradict each other on the number, duration and time of the calls. As such the two key details Cloonan cited that Ali mysteriously knew about the 9/11 plot aren’t so key after all, and so we must bear in mind the possibility of spook theatre in the Ali-9/11 conection, as we must with the rest of his story.

So who was Ali Mohamed?

This is not an easy question to answer. The evidence available points to Ali being a deep cover CIA agent, used to monitor and develop the Al Qaeda gang. His curious ability to evade capture, even as his trainees fell into the clutches of the FBI, indicates that he was protected, right up until the moment that he wasn’t, and his disappearing act since then all but proves a cover-up. The absence of any serious investigation into the Ali Mohamed story, and what it tells us about Al Qaeda, and therefore 9/11 and the whole War on Terror myth, is a hinge on which that myth swings. Dead men tell no tales, but I bet Ali Mohamed could tell us a few.

Tom Secker is an author, researcher, and filmmaker who focuses on terrorism, the security services, and declassified history. Tom is the webmaster of Investigating The Terror and Spy Culture. He is the writer, director and producer behind 7/7: Seeds of Deconstruction, and 7/7: Crime and Prejudice. His new book Secrets, Spies and 7/7 is available in both paperback and ebook versions.