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Jemaah Islamiyah (JI; lit. “Islamic Community”) is a radical Islamic movement based in Indonesia with the goal of establishing an Islamic state uniting Muslims in Southeast Asia under an Islamic caliphate. JI emerged in the late 1970s as networks behind the Darul Islam rebellions of the 1950s and 1960s were revived. The Indonesian military initially cultivated relations with movement leaders to broaden support for the ruling party as well as build a bulwark against communism after the fall of Saigon. Those leaders who could not co-opt were arrested and accused of involvement in a dubious extremist organization known as Komando Jihad. Abu Bakar Ba'asyir and Abdullah Sungkar were identified as key leaders of Komando Jihad. They were also founders in 1971 of Pesantren al-Mukmin, later known as Pondok Ngruki, an Islamic boarding school on the outskirts of Solo in central Java, where JI was born. Ba'asyir and Sungkar were tried in 1982 and sentenced to 9 years in prison; however, these sentences were overturned on appeal, and they were released in 1985. They returned to Pondok Ngruki, where, inspired by the Iranian Revolution of 1979, they again revived the network of supporters of Darul Islam, now referred to as Jemaah Islamiyah. In 1985, when the Suharto government threatened to return Sungkar and Ba'asyir to jail, they fled to Malaysia.

JI drew inspiration from the writings of Ali Shariati and Murtaza Mutahhari of Iran, Hassan al-Banna and Sayyid Qutb of Egypt's Muslim Brotherhood, and Abu'l-a'la' Mawdudi of Pakistan. The bloody repression of a demonstration by Muslims in Tandjung Priok, Jakarta's port, in 1984 and an Indonesian army attack on a JI community in Lampung, Sumatra, in 1989 contributed to radicalizing JI. In Malaysia, Sungkar and Ba'asyir began to recruit mujahideen to join the struggle against the Soviets in Afghanistan. This led to contacts with al-Gama'a al Islamiyah, the radical faction of the Muslim Brotherhood of Egypt, which was closely linked to al Qaeda. In Afghanistan, JI established links with radical Islamists from Malaysia and the southern Philippines. Between 1985 and 1995, most of JI's senior leadership fought and trained in Afghanistan and Pakistan.

After the fall of Suharto in 1998, Sungkar and Ba'asyir returned to Pondok Ngruki, where Sungkar died of natural causes. Ba'asyir became the emir (spiritual leader) of JI. In 2000, Ba'asyir established the Indonesian Mujahidin Council (Majelis Mujahidin Indonesia, MMI), bringing together all the Islamist groups in Indonesia to work for the application of Shari'a law.

JI came to public attention in November 2002 with the arrest of Amrozi, a suspect in the October 12 bombing of a Balinese night club that killed 202 people. Indonesian and Australian police traced the bombers back to Pondok Ngruki. The arrest of Imam Samudra, who had planned the operation in Bali, confirmed the Ngruki connection and revealed that JI was responsible for a series of bombings, including coordinated bombings of churches that killed 19 people and injured dozens in nine Indonesian cities on Christmas Eve 2000. In 2003, JI successfully carried out the bombing of the JW Marriott Hotel in Jakarta, killing 12 people and injuring more than 150. JI was also responsible for a bombing of the Australian Embassy in 2004. In 2003, Ba'asyir was sentenced to 4 years in prison for involvement with JI, a charge he claims is a fabrication of the CIA (Central Intelligence Agency) to discredit Islam. He was released in 2006.

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