Born in Medina, Saudi Arabia, in 1957, Khalifa served alongside Osama bin Laden as a volunteer in the jihad against the Soviet Union. Khalifa said the two were best friends and roommates during that time.
After that, however, his story branches off into two conflicting accounts.
According to Khalifa, his association with bin Laden ended there, in the late 1980s, after which he worked as an international businessman and philanthropist. In his version of the tale, he never had anything to do with any sort of terrorist ever again.
According to just about everyone else, Khalifa became a top financier for al Qaeda, with ties to the 1993 World Trade Center bombing and a plot to take down nearly a dozen U.S.-bound airliners with undetectable bombs created by the world's most dangerous terrorist, Ramzi Yousef.
On Tuesday, both stories came to an end when Khalifa was assassinated by a group of 25 to 30 gunmen, who burst into the Madagascar house where he was sleeping and killed him, according to family members.
During the late 1980s, Khalifa traveled to the Philippines and provided funding and training to the Abu Sayyaf Group, an terrorist-criminal enterprise in the southern part of the country. He also supported Muslim separatist and evangelical movements all over the region, using a network of charity organizations and legitimate businesses to hide his activities, according to U.S. and Philippines authorities.
In 1993, FBI agents investigating the World Trade Center bombing discovered several documents bearing Khalifa's name or alias, including a bomb-making manual. As the case slowly moved toward trial, other links emerged, and Khalifa was named as an unindicted co-conspirator supporting the terrorist cell that staged the bombing.
On Dec. 1, 1994, Khalifa traveled to Morgan Hill, Calif., a 20-minute drive away from an Egyptian Islamic Jihad cell based in Santa Clara. He claimed he was visiting a relative. A member of that cell, Ali Mohamed, was an FBI informant under investigation for his own role in the World Trade Center conspiracy.
Court records show Mohamed spoke with an FBI agent and a U.S. attorney investigating the Trade Center case in New York on Dec. 9. On Dec. 16, the State Department revoked the Saudi's visa.
Khalifa was arrested at the San Francisco airport as he prepared to leave the country. His traveling companion was a senior al Qaeda operative named Mohamed Loay Bayazid, who had tried to purchase uranium on behalf of al Qaeda just one year earlier, according to court testimony.
The FBI searched Khalifa's luggage and found a treasure chest of intelligence -- terror training manuals written by Khalifa himself, and more importantly, address and phone books with listings for al Qaeda's terrorist elite, including bin Laden himself.
Agents also found clues to the location of the world's most dangerous terrorists -- Ramzi Yousef, the mastermind of World Trade Center bombing, and Khalid Shaikh Mohammed, future architect of the September 11 attack.
Khalifa's notes contained the pager number for Wali Khan Amin Shah, a close associate of bin Laden who was conspiring with Yousef and KSM to bomb a dozen U.S. bound airliners over the Pacific Ocean during a two-day spree scheduled for January 1995.
Phone records showed that Khalifa had called Khan's apartment several times in November. Yousef was building bombs for the attack in a different apartment at the same address, a few floors up. A source close to the investigation said an address for the location was also found on Khalifa's luggage.
Three weeks after Khalifa was arrested, the Philippines police raided Yousef's apartment. At the time, authorities said they discovered the bomb factory as the result of a chance fire set by Yousef while mixing chemicals. But the FBI had forwarded its Khalifa intelligence to the Philippines police two days before the raid.
After searching Yousef's apartment, police set a trap and captured Wali Khan Amin Shah using the pager number taken from Khalifa's luggage. The source of the number was not disclosed during Yousef's trial.
Yousef and Khalid Shaikh Mohammed fled the country, but Yousef was arrested within weeks in Pakistan. Yousef later told a cellmate that Shah been betrayed by an informant and vowed the informant would be killed, according to FBI documents obtained by the late Stephen Dresch, an independent investigator.
Could Khalifa have been the informant?
At minimum, the information in Khalifa's luggage was responsible for the arrest of Shah, and likely the exposure of Yousef's entire cell. But subsequent events raise serious questions about whether things might have gone further.
At the time of his arrest, Khalifa was wanted by the government of Jordan for allegedly training a terrorist cell responsible for a series of cinema bombings there. Secretary of State Warren Christopher personally demanded Khalifa be deported to Jordan, a request that was expedited by the Justice Department.
As a result, Khalifa was blocked from asking the INS to deport him back to his native Saudi Arabia. The paperwork came down within hours of the raid on Yousef's bomb factory.
In March, after Yousef had been captured and returned to the United States, the U.S. Attorney's office in San Francisco agreed to return the contents of Khalifa's luggage. Although FBI agents carefully photocopied all the material, the most direct evidence tying Khalifa to Yousef's plot was simply handed back to the alleged terrorist.
In April, after the Oklahoma City bombing, Khalifa abruptly dropped his opposition to the deportation proceedings and cut a deal with the INS to be returned to Jordan. In exchange for his cooperation, the INS agreed to strike all terrorism charges from his record. Khalifa's full name was never disclosed during Yousef's trial, even though his phone calls to Shah were carefully logged into the record.
Khalifa was deported on May 3, but he wasn't removed from U.S. custody. Instead, according to Bureau of Prisons records obtained under the Freedom of Information Act, Khalifa was transferred to the custody of an unidentified U.S. government agency which maintained jurisdiction over him until August. BOP officials refused to disclose the identity of the agency.
In July, Khalifa was cleared by a Jordanian court after a witness against him recanted. He was then sent back to Saudi Arabia, where he was greeted at the airport by Saudi officials, according to Michael Scheuer, former head of the CIA's bin Laden unit, in his book "Through Our Enemies' Eyes."
Although rumors of his continued involvement in terrorism were plentiful, Khalifa maintained a low profile for several years after his arrest. He was detained by Saudi authorities after September 11, according to the New York Times, but was released without charge six months later.
He opened a seafood restaurant in Jeddah and eventually started talking to journalists, serving as a major source for prominent authors including Peter Bergen and Lawrence Wright.
During these interviews, Khalifa focused on his early years with bin Laden and steadfastly denied any involvement with terrorism. Because he was a rare source who had been close to bin Laden, the media focus shifted to his tales of the old days. The extensive and specific evidence implicating him as an accessory to Ramzi Yousef faded from memory as he achieved a certain celebrity in the role of "reformed terrorist."
But on Tuesday, Mohammed Jamal Khalifa's past caught up with him.
During a business trip to Madagascar, Khalifa was killed in a large-scale attack by gunmen who ambushed him in the house where he was staying. The team of 20 to 30 gunmen stole his computer and a briefcase, according to published reports citing Khalifa's brother as the source.
Khalifa was in Madagascar dealing with issues at a precious stones mine he owned there, according to published reports.
Obvious questions remain. Who killed Khalifa, and why?
It's possible that Ramzi Yousef's threat of revenge against an informer has finally been realized. It would have been difficult (but by no means impossible) to strike against Khalifa in Saudi Arabia, especially if he was under the protection of authorities there.
Perhaps by emerging from his nest, Khalifa opened himself to retribution. But a small battalion of gunmen would not be especially consistent with al Qaeda's modus operandi, and other possibilities remain.
CNN analyst Nic Robertson on Wednesday suggested the other obvious scenario -- that the attack may have originated with a state-sponsored intelligence service. The size of the team, and the fact that the attackers stole Khalifa's computer and papers, might point to a botched snatch-and-grab operation.
The question then: Which service, and why?
There are other possibilities. It may have been a simple robbery, as his family claims. Or it may have been a hit taken out by a rival sect or terrorist group. If the latter (which I think unlikely), the attack would speak volumes about Osama bin Laden's weakness.
Answers will come slowly, if at all. It's unclear what sort of investigation is planned, and whether the results will ever become public.
In death as in life, Khalifa's secrets remain untold.
Dossier of FOIA, Court Records on Mohammed Jamal Khalifa Deportation