Formed in the mid-1980s by 2 Indonesian clerics, JI became a terrorist organization when one of the co-founders, Abdullah Sungkar, came into contact with Osama bin Laden and al Qaida. JI has since spread to include terrorist cells in every country in Southeast Asia and in Australia. The principal goal of the organization is the creation of a unified Southeast Asian Islamic state which they want to stretch from southern Thailand, through the Malay Peninsula, encompassing Singapore, and across the Indonesian archipelago into the southern Philippines. They are most active in Indonesia, Malaysia, Thailand and southern islands of the Philippines, where they claim to wage holy war against agents of "Western imperialism," and others who resist their movement.

Currently led by cleric Abu Bakar Bashir, the JI is thought to be responsbile for the October, 2002 bombings in Bali, the Marriott bombing in August 2003, and a failed plot to bomb US and Israeli embassies and the British and Australian diplomatic buildings in Singapore in December 2001.