For some, it was a short jump from anger at Christians in Maluku to anger at all Christians and at Indonesia's secular government; from concern about domestic matters to an interest in the grand conspiracy theory spun by Al Qaeda.
Samudra and his colleagues worked hard to encourage this evolution in thinking. They'd been whispering in the ears of young men for years, winning one or two converts at a time. Now Maluku had given them a megaphone. They recruited young men to fight in Maluku, and from them culled future operatives. The war was also used to build sympathy for their views in the general Indonesian population.
"Samudra? Well, he simply hates Americans,'' says Lt. Col. Yatim Suyatmo, chief spokesman for the Bali police. "But for many of the people under him, their anger was focused by speeches about the suffering of Muslims in Ambon."
Taufik Abdul Halim was a typical new recruit. In June 2000, the young Malaysian and eight others - spurred by videos of men suffering - arrived in Maluku from the porous eastern border on Borneo. Today Halim languishes in a Jakarta jail, without the bottom half of his right leg.
His trial documents show how Maluku served as a gateway to terrorism.
In the village of Siri Sori, Halim fought under a commander Haris Fadillah, famous for his aggressive tactics against Christian villages - and the father-in-law of Omar al-Faruq, accused of being a top liaison between Al Qaeda and JI.
At the end of February 2001, Halim and a small group of comrades were sent to Jakarta. There they were met by Edi Setiono, a JI member who asked Mr. Halim's group if they'd be willing to participate in attacks on three Jakarta churches.
The men agreed, and the bombings were carried out on July 22 and August 1. "Our motivation ... was revenge," Halim said in his deposition. "In Eastern Indonesia, many Christians are involved in slaughtering the Muslim population."