But the MMI also played a more traditional political role. Bashir and other MMI leaders had a two-hour meeting with Vice President Hamzah Haz this week. The vice president told them he shares their dream of introducing Islamic law to Indonesia, says MMI member Deliar Noer, who attended the meeting.
Bashir isn't the only militant leader who has been able to make an impact on Indonesia's stability.
Last week, the paramilitary group Laskar Jihad ignited another wave of killing in Maluku province, where thousands have been killed in sectarian violence since 1999. Indonesian officials had hoped that a three-month lull in the violence and a peace agreement signed in February meant the worst was over.
But militants such as Bashir and Laskar Jihad leader Jaffar Umar Thalib had attacked the peace deal and vowed to bring it down. Last Friday, Mr. Thalib, who has also held meetings with Vice President Haz, led prayers at the main mosque in the provincial capital of Ambon and urged renewed attacks on Christians, calling the peace deal "treasonous."
Bashir says that the MMI and the Laskar Jihad coordinate their activities and that Thalib is doing "good work" in Ambon. Government officials say that Thalib, like Bashir, has remained free because the government worries that arrests could be counterproductive.
"The official government line is that, if they go too hard, there will be a backlash,'' says David Martin Jones, a politics professor at the University of Tasmania in Australia. "This is not a very good strategy in terms of preserving rule of law. The message certainly seems to be that you can get away with murder.''
Singapore and Malaysia say that Bashir leads the Jemaah Islamiyah (JI), a terror group trained and financed by Al Qaeda. Nearly two dozen members of the group were arrested in the two countries last year for conspiring to blow up the US Embassy in Singapore.