Jemaah Islamiyah are suspected of having executed the October 12 2002 Bali car bombing in which 202 people, mainly holidaymakers, were killed. They are also suspected of committing the Zamboanga bombings.
JI was established as a loose confederation of several Islamic groups. Sometimes around 1969, two men, Abu Bakar Bashir, and Abdullah Sungkar, began an operation to propogate the belief of Darul Islam, a conservative strain of Islam.
Bashir and his friends created a pirated radio outfit to preach to the poor and oppressed in Indonesia. Bashir created a boarding school in Java. The school's motto was, "Death in the way of Allah is our highest aspiration."
He and his followers escaped to Malaysia in 1982. He recruited people from Indonesia, Malaysia, Singapore, and the Philippines. The group oficially named itself Jemaah Islamiyah around that time period.
The members of JI ranted and distributed pamphlets, but committed relatively few terrorist acts. Bashir preached jihad but he would do very little violent action. This changed in the 1990's.
Bashir met Riduan Isamuddin, a.k.a. Hambali sometime in the early 1990's at a religious school that Bashir set up. Bashir became the spiritual leader of the organization while Hambali became the military leader.
Hambali wanted a large Islamic caliphate to be established across Southeast Asia, incorporating Indonesia, Malaysia, Singapore, Thailand, the Philippines, Brunei, Cambodia, and Thailand. Such a state would have a population of about 420 million (using CIA World Factbook population counts). It would have a strangle-hold over the South China Sea shipping lanes which are a gateway between parts of Asia and the Indian Ocean. It would also have a significant air-space and would potentially affect trade between India, Africa, and Australia.
JI first formed itself into a group of terrorist cells that provided financial and logistical support when needed to Al-Qaida operations in Southeast Asia. Hambali formed a front company called Konsojaya to help launder money to such plots, including the Operation Bojinka plot, which was foiled on January 6, 1995.
In 2000, Hambali ran a series of bombings of Christian churches. More attention went on the group after the Bali nightclub bombing. Another high profile attack was the bombing of the J.W. Marriott hotel in Jakarta.
Bashir was arrested by the Indonesian police and was given a light sentence for treason.