U.S and Filipino investigators accuse him of once being an important lieutenant of Osama bin Laden's Al-Qaida organization, which was based in Sudan at the time he allegedly was involved in terrorist plots.
Khalifa used the alias Abu Barra.
He started the Benevolence International Corporation in the Philippines in 1988, apparently to recruit people for the war against the Soviets. He was back in 1991. Benevolence International Corporation claimed to have been an import-export company. In 1992, that group folded visible operations while another group known as the Islamic Benevolence Committee renamed itself to Benevolence International Foundation.
The first glimpse U.S. authorities had of Khalifa came in 1992, when Ramzi Yousef and Ahmed Ajaj entered the United States on a false passport. Ajaj was arrested when his passport was found as false and when bomb-making manuals were found in his luggage. Khalifa's alias Abu Barra appeared on the manual. Yousef was released and was told to come back to the INS in one month, as holding cells were overcrowded. He was able to slip away and plot the 1993 World Trade Center bombing.
What was left of the Benevolence International Corporation allegedly gave logistical support to terrorists. The remains of the Benevolence International Corporation have been accused of assisting the 1993 World Trade Center bombing and the Operation Bojinka plot that was foiled in 1995. The U.S. government claims that he came to the Philippines to support Abu Sayyaf. Khalifa had married a local woman, Alice "Jameelah" Yabo, and frequently exited and entered the country for "business" reasons. Yabo was the sister of Abu Omar. Philippines authorities say that Khalifa moved money to Abu Sayyaf to pay for supplies. They also say that he was frequently in contact with Riduan Isamuddin, aka Hambali.
Khalifa also ran the International Relations and Information Centre. Money was embezzled through the bank account of Omar Abu Omar, an employee at the centre, to an account under the name of Adam Salih, an alias of Ramzi Yousef.
Khalifa had started several other groups, including the Khalifa Trading Industries, which U.S. investigators claim that were front organizations.
Khalifa was the regional director of the Philippines for the International Islamic Relief Organization.
In December 1, 1994, Khalifa met Mohamed Loay Bayazid, the president of Benevolence International Foundation, in the United States. Khalifa and Bayazid were arrested in December 14, 1994 in Mountain View, California on charges related to the 1993 World Trade Center bombing. Khalifa was planning to fly to the Philippines.
When the FBI looked inside Khalifa's luggage, they found manuals in Arabic on training terrorists, which covered subjects such as bomb-making and other violent activities. Khalifa claims that his possession of the materials was in innocence.
They also found a personal organizer with several contacts. One phone number was for Wali Khan Amin Shah, a member of the Manila cell, which was plotting Operation Bojinka at the time. There was also a listing for an unknown man, who might have been Khalid Sheik Mohammed. Khalifa was placed in solitairy confinement and the contents of his luggage were logged and edited.
On January 6 and January 7, 1995, Operation Bojinka was discovered after a fire at Yousef's Manila apartment. Investigators found evidence related to the plot. Abdul Hakim Murad, who was arrested at the apartment, had five phone numbers pointing to Khalifa. They also found logs of phone calls to and from Khalifa before his arrest and contact information on Ramzi Yousef's computer.
Khalifa first fought his deportation by suing the government. He then got his San Francisco lawyers to prepare a lawsuit requesting for the return for his belongings.
On April 18, the conviction in Jordan was overturned as a key witness recanted his testimony.
Khalifa now lives in Saudi Arabia. He occasionally makes a media statement proclaiming his innocence. He publicly condemned Osama Bin Laden after the September 11, 2001 Attacks and has publicly distanced himself from them.
If Khalifa was a key lieutenant in Osama bin Laden's Al-Qaida terrorist network, as U.S. and Filipino officials believe he is, it appears that he has now retired.