He came to the United States working as a translator for Ayman al-Zawahiri, who toured California mosques to raise money to fight the Soviet invasion of Afghanistan. While there, Zawahiri encouraged him to infiltrate the United States, claiming to be defecting to the United States. When he simply walked into the CIA office in Cairo and asked to speak to the station chief to offer his services, the Americans assumed he was an Egyptian spy, but nevertheless recruited him to be a junior intelligence officer. When tasked to infiltrate a mosque with ties to Hezbollah, he instead informed the imam he was an American spy intending to collect information. Another loyal American spy was also in the congregation and he reported Mohamed to the CIA, which dismissed him and sought to ban him from entering the United States. However, he later enlisted in the Special Forces of the U.S. Army, who sent him to the Special Warfare school and encouraged him to pursue a doctorate in Islamic Studies to teach courses on the Middle East.
In the 1980s Mohamed trained anti-Soviet fighters en route to Afghanistan. FBI special agent Jack Cloonan called him "bin Laden's first trainer". Mohamed was charged with the August 7, 1998 bombings of the United States embassies in Nairobi, Kenya and in Dar es Salaam, Tanzania. In October 2000, he pleaded guilty to five counts of conspiracy to kill nationals of the United States and to destroy U.S. property.
Mohamed has been described as "Six-foot one, 200 pounds, and exceptionally fit, ... a martial artist and skilled linguist who spoke fluent English, French, and Hebrew in addition to his native Arabic. He was disciplined, clever, and gregarious, with a marked facility for making friends."
Mohamed was a major in the Egyptian army's military intelligence unit, until being discharged for suspected fundamentalism in 1984. He enlisted in the U.S. Army and used U.S. military information to train al-Qaeda and other Muslim militants, and write al-Qaeda's multivolume terrorist training guide.
During the 1980s, Ali Mohamed was involved in the training of the anti-Soviet Afghan mujahideen. Mohamed conducted training during the war to small classes which included Osama bin Laden (Past leader of al-Qaeda), Ayman al-Zawahiri (current leader of al-Qaeda), and the terrorist members responsible for the bombings of the two U.S. embassies in Africa. His training took place in training camps in Afghanistan. He also spent much time fighting in Afghanistan himself against the Soviet forces.
After moving to the United States and joining the U.S. Army, Ali Mohamed gathered intelligence about the Army and U.S. infrastructure during his time as a drill instructor and support Sergeant. In 1988, Ali returned to Afghanistan to fight the Soviet Union. During this time, it is widely believed that he continued to train cells of terrorists using the information learned while living in the U.S. After a month he returned to the United States.
In 1990, Ali Mohamed returned once again to Afghanistan, and once more, trained terrorist in the art of guerrilla and unconventional warfare which include hijacking, suicide bombing, kidnapping, and IED bombs.
During this time, it is also known that he began planning the embassy bombings with Osama bin Laden and Ayman al-Zawahiri. Later on, Ali Mohamed was key in assisting the movement of al-Qaeda from Afghanistan to Sudan. He moved back and forth, assisting in key movements of camps.
In 1992, Ali Mohamed made several trips to Afghanistan as part of the training of terrorist cells. During that year he made at least 58 trips whilst under the surveillance of the CIA. He fought and trained in the civil war among the Afghan mujahideen that ensued after the defeat of the Soviet forces. In this time he trained the al-Qaeda generals in the art of intelligence warfare. This included surveillance, counter-surveillance, assassinations, kidnapping, codes, and ciphering codes.
The system of cell structures and groups within a terrorist faction was developed by Ali around this time as a means of making it harder to destroy terrorism by spreading members out. Bin Laden and Ali Mohamed worked closely to create cells in Tanzania and Kenya to help prepare for the bombings of the embassies. After planning ended, Ali moved to Nairobi where he helped set up a terrorist cell. He funded the cell by creating companies in the fishing and car business. After setting up, he moved back to Afghanistan where bin Laden and other members of al-Qaeda discussed plans for the bombings and other information.
In 1984 Mohamed offered his services to the CIA in Cairo station and was stationed in Hamburg, Germany. There he "entered a mosque associated with Hezbollah and immediately told the Iranian cleric in charge that he was an American spy assigned to infiltrate the community." The mosque had already been penetrated and his announcement was passed on to the CIA, which, according to Lawrence Wright, "terminated Mohamed" and "sent out cables labeling him highly untrustworthy." By this "time, however, Mohamed was already in California on a visa-waiver program that was sponsored by the agency itself, one designed to shield valuable assets or those who have performed important services for the country."
In America he married an American woman from Santa Clara, California after a 6-week courtship and became a U.S. citizen. He enlisted in the U.S. Army and managed to get stationed at the John F. Kennedy Special Warfare Center and School at Fort Bragg, North Carolina until 1989. "His awed superiors found him 'beyond reproach' and 'consistently accomplished'."
According to Cooperative Research, Mohamed was a Drill sergeant at Fort Bragg, and was hired to teach courses on Arabic culture at the John F. Kennedy Special Warfare Center and School.
In 1988 Mohamed informed his superior officers in the U.S. Army that he was taking some leave time to fight Soviets in Afghanistan. "A month later, he returned, boasting that he had killed two Soviet soldiers and giving away as souvenirs what he claimed were their uniform belts."
Mohamed's commanding officer, Lt. Col. Robert Anderson, said he wrote detailed reports aimed at getting Army intelligence to investigate Mohamed — and have him court-martialed — but the reports were ignored.
"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 said. "That just doesn't happen."
It was equally unthinkable that an ordinary American GI would go unpunished after fighting in a foreign war, he said.
Anderson said all this convinced him that Mohamed was "sponsored" by a U.S. intelligence service. "I assumed the CIA," he said.
Mohamed also took maps and training manuals off base to downsize and copy at Kinko's and used them to write al-Qaeda's multivolume terrorist training guide that became a playbook.
Mohamed also conducted clandestine military and demolition training through the Al Kifah Refugee Center. While in the United States, he helped train a number of jihadis, like El Sayyid Nosair and Mahmud Abouhalima, who assisted Ramzi Yousef in his 1993 attack on the World Trade Center.
In the early 1990s Mohamed returned to Afghanistan, where "he trained the first al-Qaeda volunteers in techniques of unconventional warfare including kidnappings, assassinations, and hijacking planes, which he had learned from the American Special Forces." According to FBI special agent Jack Cloonan, in one of Mohamed's first classes were Osama bin Laden, Ayman al-Zawahiri, and other al-Qaeda leaders.
In 1993 Mohamed also traveled to Africa to survey embassies in Africa such as the Nairobi, Kenya embassy which Al-Qaeda later bombed. He became an FBI informant.
In 1994, al-Qaeda operative Mohammed Atef refused to allow Mohamed to know which name and passport he would be traveling under, expressing concerns that Mohamed could be working with the American authorities.
In a televised interview Mohamed explained his rationale for his efforts: "Islam without political dominance cannot survive."
In 1998, two weeks after the bombings, FBI agents searched Ali’s apartment. They found evidence of terrorist activities which included plans and scripts of Al-Qaeda training. Ali Mohamed had made plans to leave the country to meet with Osama bin Laden. However he was subpoenaed to testify in the trial of the other suspects. The same day of the trial, Mohamed was arrested as a key suspect in the embassy bombings.
Just before the trial, the FBI ordered that a polygraph test be conducted on Mohamed but it later was discarded after Mohamed struck a guilty plea to receive life sentence without parole. The deal between Mohamed and the government was struck on October 13, 2000. He was charged with 5 counts of conspiracy. The sentencing trial as shown below identified the specific counts that Ali Mohamed was to be indicted. The first count charges a violation of title 18, under the United States code, section 2332(b) which is the conspiracy to kill nationals of the United States of America wherever they are in the world. In such case, the citizens were located at the embassy of the United States of America in Kenya and Tanzania. The second count was conspiracy to murder, kidnap and maim outside the United States. This would include the conspiracy to kill US nationals employed by American military in the embassies. Count three was conspiracy to murder, through violating sections 1114 or 1116. Under section 1116, Ali sought to kill United States government employees under their roles as employees of the United States of America. Count five charges a conspiracy to destroy buildings or property owned or leased by the United States government. The government proved that Ali attempted and planned to destroy or damage buildings or property owned or leased by the United States government. Finally, count six is the conspiracy to destroy national defense utilities of the United States government. Ali told the court that he had been involved with the Egyptian Islamic Jihad in the 1980s and was introduced to Osama bin Laden in the 1990s. “In 1992, I conducted military and basic explosives training for al Qaeda in Afghanistan. Among the people I trained were Harun Fadhl and Abu Jihad. I also conducted intelligence training for al Qaeda. I taught my trainees how to create cell structures that could be used for operations”. Ali then included information in the events leading up to the embassy bombings; “In the early 1990s, I assisted al Qaeda in creating a presence in Nairobi, Kenya, and worked with several others on this project. Abu Ubaidah was in charge of al Qaeda in Nairobi until he drowned. Khalid al Fawwaz set up al Qaeda’s office in Nairobi. A car business was set up to create income. Wadih el Hage created a charity organization that would help provide al Qaeda members with identity documents”. Ali then told the court that he was asked by bin Laden to identify possible targets of which he conducted surveillance on the American Embassy building.
In October 2001, the Raleigh News & Observer noted that Ali Mohamed may be cooperating with the U.S. government. "Defense lawyers and many other observers believe that Mohamed, who has not yet been sentenced, is now cooperating with the United States, though the government has never confirmed this. When he is sentenced he could receive as little as 25 years under his plea agreement." In his book The Mission, The Men, and Me: Lessons from a Former Delta Force Commander, former Delta Force commander Pete Blaber indicates he met Ali Mohamed who gave him information on how to infiltrate Afghanistan, find al-Qaeda commanders, and operate in country undetected in late 2001.
Further news sources in 2001 seem to suggest that Ali Mohamed is providing information on al-Qaeda in an attempt to reduce his sentence, and that his sentencing "has been postponed indefinitely." In 2006, Mohamed's wife, Linda Sanchez, was reported in 2006 as saying, "He's still not sentenced yet, and without him being sentenced I really can't say much. He can't talk to anybody. Nobody can get to him. They have Ali pretty secretive...it's like he just kinda vanished into thin air."
In 2011, former FBI agent Ali Soufan confirmed that Mohammed is still awaiting sentencing.