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Al-Faruq maintained close ties with Abu Zubaydah and al-Qaeda. In the late 1990s al-Faruq slipped into Indonesia to take control of al-Qaeda's operations in Southeast Asia. Across a belt of territory stretching from Myanmar (formerly Burma) to eastern Indonesia, radical Islam was on the rise, with militants occupying swaths of the region's steamy jungle terrain. In Indonesia the fall of the dictator Suharto in 1998 left the world's most populous Islamic country in a state of turmoil and turned it into a fertile breeding ground for potential al-Qaeda terrorists. Al-Faruq married Mira, the daughter of a former Islamic activist, and linked up with an Indonesian businessman named Agus Dwikarna, who was active in the Indonesian Mujahedin Council (MMI). A purportedly nonviolent political organization, the MMI was founded by Abubakar Ba'asyir--the Indonesian cleric also believed to be the spiritual leader of JI, which is run by Ba'asyir's former student Riduan Isamuddin, known as Hambali. In addition to his alleged links to scores of bank robberies and murders in Malaysia, Indonesia and the Philippines, Hambali is believed to have colluded with al-Qaeda since 1995. Western intelligence officials say he played host to two of the Sept. 11 hijackers during their trip to Malaysia in 2000. Hambali is thought to have gone into hiding, but his organization remains active. In an interview with TIME, JI members said al-Qaeda operatives continue to meet with radical groups in the region, and, according to one of them, JI boasts a cadre of 20 suicide bombers "waiting and ready to carry out attacks if instructed."
While intelligence officials have long believed that Hambali ran the day-to-day operations of JI, al-Faruq told the CIA that Ba'asyir was just as eager to work with al-Qaeda, even dispatching his aides to procure weapons and explosives for al-Faruq and his cronies. Last week Ba'asyir repeated his longstanding denial of connection with terrorist groups. "I don't have any link whatsoever with al-Qaeda," he told TIME, "but if al-Qaeda's struggle is for the best interest of Islam, I support it."
According to a foreign intelligence report, al-Faruq told the CIA he helped Dwikarna establish Laskar Jundullah, a militant Islamic group dedicated to forming an Islamic state and involved in attacks on Christian villages in central Sulawesi province. Beginning in mid-1999, al-Faruq claims, he launched a succession of audacious but generally unsuccessful terrorist plots. In May of that year, al-Faruq met with several potential accomplices at a villa in west Java and hatched a plan to kill current Indonesian President Megawati Sukarnoputri, who was then a candidate for the presidency. The plot involved buying weapons in Malaysia and the Philippines, but the group failed to get the guns into Indonesia. Last year a second assassination scheme--it involved detonating a bomb at a meeting of Megawati and other ruling party leaders--fizzled when the designated bomber lost his leg and was arrested after the bomb he was carrying blew up prematurely near the Atrium Mall in Jakarta in August 2001.