In eastern Indonesia, on the islands of Maluku and Sulawesi, ongoing fighting between Christians and Muslims has left more than 10,000 dead, and up to half a million refugees. Attempts at reconciliation between the communities, which had lived in peace and cooperation for many years, were succeeding until mid 2000, when the Laskar Jihad, a radical Islam militia from the island of Java, intervened.
Using thousands of trained and uniformed militiamen, often armed with automatic rifles, the Jihad transformed local conflict into full-scale religious cleansing. It swept through Maluku, burning villages and killing and driving out Christians (as well as the few Hindus and Buddhists) while Indonesian government security forces stood by.
The Jihad then moved to Sulawesi. In July 2001, thousands of jihadists began arriving, after officially informing the local governor of their coming. They said publicly that their goal was to drive out all Christians and institute an extreme version of Islamic sharia law. Violence is ongoing in Sulawesi, with sniper attacks, bombings and church burnings. On Aug. 12, the village of Sepe, with a population of about 1,250, was totally burned down.
http://www.freedomhouse.org/religion/country/indonesia/Terror's Not New to Indonesia.htm