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Around that time, al-Faruq began running into trouble. He had been living near Dwikarna in Makassar, in South Sulawesi province, but because of his poor language ability, he never managed to acquire an Indonesian passport. In mid-2001, immigration authorities detained al-Faruq temporarily and prepared to deport him. Al-Faruq skipped town, heading to Cijeruk with Mira and their baby daughter. After Sept. 11 he stayed in contact with Abu Zubaydah during the U.S. military campaign against al-Qaeda in Afghanistan. Abu Zubaydah told al-Faruq that he should plan to return soon to Kuwait, but in the meantime, al-Faruq was to set in motion new terrorist missions. Knowing the U.S. Navy was scheduled to conduct joint exercises in the Surabaya harbor in late May, al-Faruq plotted a suicide attack against a U.S. ship, similar to the deadly al-Qaeda operation against the U.S.S. Cole in Yemen in 2000. He drafted a Somali operative named Gharib to help find Arabs willing to participate in the suicide mission. But when he failed to recruit enough operatives to carry out the plan, al-Faruq had to scrap it.
What al-Faruq may not have known was that in early 2002, U.S. and regional intelligence officials had picked up his signal. On Feb. 25, according to intelligence reports, the CIA informed regional counterparts that three Indonesian-based Islamic militants had established a training school for terrorists on the island of Borneo. Indonesian investigators discovered that four MMI operatives, including al-Faruq, had held training exercises at the same location. While al-Faruq initially managed to stay beyond the reach of authorities, some of his closest associates ran out of luck. In March Dwikarna was arrested in Manila after airport security guards discovered plastic explosives and detonation cables in his suitcase; the next month U.S. and Pakistani forces seized Abu Zubaydah in Faisalabad, Pakistan. A regional intelligence brief says on April 27 the CIA reported that the same cell-phone number, 081-2957-6852, had been programmed into the handsets of both Dwikarna and Abu Zubaydah. The number was al-Faruq's.
Investigators soon realized al-Faruq was a man with connections. An al-Qaeda prisoner at America's Camp X Ray in Guantanamo Bay, Cuba, also had al-Faruq's number. The same intelligence report says the CIA traced a number dialed by Fathur Rohman al-Ghozi, an Indonesian JI militant arrested for suspected involvement in last December's Singapore bomb plot, back to al-Faruq. In May, the report continues, the CIA found that Ibin al-Khattab, the late Chechen commander with ties to al-Qaeda, had once placed a call to al-Faruq on his cell phone. On May 2, shortly after discovering that al-Faruq had acquired a fake Indonesian passport, the Indonesian government authorized agents to arrest him. Intelligence reports say that on May 23, U.S. interrogators questioning Abu Zubaydah showed him a picture of al-Faruq. Abu Zubaydah quickly identified his old friend as "al-Faruq al Kuwait." He then told his inquisitors the tangled tale of al-Faruq's quest to turn Southeast Asia into an al-Qaeda stronghold. Two weeks later, authorities swooped in on al-Faruq at a mosque in Bogor. Says Susilo Bambang Yudhoyono, the country's chief security minister: "It was quite rapid work."