The Jemaah Islamiyya (JI) was established as an underground, secret militant Islamist organisation in 1993 in Malaysia by Indonesian clerics Abdullah Sungkar and Abu Bakar Ba'asyir. Sungkar and Ba'asyir, who had fled Indonesia in 1985, returned to Indonesia in 1999 following the revoking of the subversion law. Sungkar died in November 1999 and was succeeded by Ba'asyir as the organisation's emir.
JI traces its roots to the Darul Islam (DI) rebellions which sought to transform Indonesia into an Islamic state. Its ideology is salafi-jihadi drawing upon the thinking of DI emir Kartosuwirjo, jihadi leaders Abdullah Azzam and Osama Bin Laden and, of course, Sungkar and Ba'asyir. The organisation's aim between 1993 and 2002 was to establish a South-East Asian Islamic state starting with Indonesia but ultimately encompassing Thailand, Indonesia, Malaysia, Singapore, Brunei, and the Philippines. Accordingly it had a regional structure with mantiqi I (region I) covering Singapore and Malaysia; mantiqi II covering Indonesia except Sulawesi; mantiqi III covering Mindanao, Sabah, and Sulawesi; and mantiqi IV covering Papua and Australia. The mantiqis were further divided into districts or wakalah, sub-districts and cells.
Counter-terror operations following the 2002 Bali bombings destroyed much of JI's financial, command, decision-making structure and regional structures. They also exacerbated internal tensions, which had been evident since Ba'asyir's succession as emir, over the strategy for achieving an Islamic state. Ba'asyir had pushed to open up the movement, taking advantage of the new openness of post-Suharto Indonesia to struggle politically for an Islamic state. However, a group of younger militants, including al-Qaeda linkman Riduan Isamudin (widely known as Hambali), saw this as anathema to Sungkar's strategy of an underground, primarily military struggle. It was this younger faction that resorted to bombings and suicide bombings with high grade explosives such as C4 and RDX under the guidance of the Malaysian engineer and university lecturer, Azhari Husin, and Nurdin Mohamed Top. With the repeated arrest, trial and imprisonment of Ba'asyir, the younger militants seized upon the opportunity to replace Ba'asyir as emir first by Abu Rusdan and then by Abu Dujana.
The killing of large numbers of Muslims in the bombings after 2002 eroded much of the sympathy JI had in the broader Indonesian population. Coupled with the arrest and imprisonment of hundreds of JI members, the capture of Abu Dujana in 2006, and the defeat of JI militants in Poso in 2007, this led to a reorientation of JI toward proselytisation. Indeed, JI became so quiet that many assumed it had ceased to exist as an organisation. However, in 2013 JI started to gain renewed support in the context of the Syrian civil war. For a detailed discussion of JI see Solahudin, The Roots of Terrorism in Indonesia: From Darul Islam to Jema'ah Islamiyya (Sydney: UNSW Press and Lowy Institute, 2013).See also ICG, Al-Qaeda in Southeast Asia: The case of the 'Ngruki Network' in Indonesia, Asia Briefing 20, August 2002 and ICG, Indonesia Backgrounder: How the Jemaah Islamiya Terrorist Network Operates, Asia Report 43, December 2002. ICG, Terrorism in Indonesia: Noordin's Networks, Asia Report 114, May 2006.