He was seized from a hospital bed after international condemnation of the Bali bombings, the second time the 65-year-old has seen the inside of a jail cell in the last quarter of a century.
General Suharto’s repressive government first put Bashir behind bars between 1978 to 1982 for inciting people to reject the secular national ideology in favour of an Islamic state.
Prosecution lawyers claim the preacher officially founded today’s Jamaah Islamiyah (JI) while in Malaysia in 1993.
But the roots of JI Islamist movements in Indonesia go back to when the country won its independence from Dutch colonialists in a bitter war more than 50 year ago.
Born in 1938, in East Java, Bashir has spent decades preaching Islamic unity. His consistent theme has always been that Islamic communities are the necessary precondition for setting up an Islamic state.
Numerous local groups in the 1960s and 70s were known broadly as the Jamaah Islamiyah (Islamic Association) and were supported by Bashir and like-minded activists.
Bashir fled to Malaysia in 1985 when the Supreme Court granted a government appeal for an additional prison sentence.
Islamist groups were sometimes manipulated by Indonesia’s military government until 1998 as a means to counter internal communist and democratic opposition.
Islamic nation preaching
But by 1990, according to Singaporean officials, Bashir was travelling around Malaysia preaching the cause of a state joining Muslims in Malaysia, Indonesia, Singapore and parts of the Philippines and Thailand.
1938 Born in East Java
While some JI members are believed to have dispatched volunteers for training in the camps run by armed groups in Afghanistan and Pakistan in the early and mid-1990s, Bashir remained an ideological preacher.
In 2002, Vice President Hamzah Haz visited the cleric’s Islamic boarding school at Ngruki in Central Java. “There is no such thing as an international terrorist network in Indonesia,” Haz declared after talks with Bashir on “Islam’s peaceful message”.
Barely a week later Bashir was placed under arrest despite his condemnation of the Bali bombing as a “brutal act”.
Western governments headed by the US urged Jakarta to reinstate the repressive apparatus used by the previous government to quash opposition.
These measures were used for the first time to justify his arrest, although intelligence officials and police both said there was no evidence linking him to the Bali bombing.
Instead, he was detained in connection with the earlier Christmas 2000 bombings.
Later charges included organising a foiled bombing campaign in Singapore, an aborted plot to kill Megawati Sukarnoputri before she became president and of seeking to topple Indonesia’s government.
On 23 April 2003 Bashir went on trial, insisting that “the whole thing is slander made up by the United States.”
Although Bashir has described al-Qaida leader Usama bin Ladin as a “true Muslim fighter” – he insists he is not involved in organised violence.
He claims he was framed by the United States and other “infidel enemies” of Islam because he campaigned for Islamic sharia law in Indonesia.
Bashir publicly pushed for sharia law after returning to Indonesia in 1999, sitting on the executive of the Mujahidin Council in Yogyakarta with the aim of turning the country into an Islamic state.