In 1972, he along with his friends founded the Al Mukmin boarding school, in Ngruki, near Solo, Central Java.
At the time of initiation, the activity of Al Mukmin was limited to religious discussion after mid-day prayer. The increasing demand led it to become a Madrasah or Islamic School and later Pesantren or Islamic boarding school.
Bashir was accused and arrested for actively supporting Sharia and promoting an Islamic State. He was accused of inciting people to reject the Indonesian national philosophy Pancasila which promotes religious pluralism. He was also charged of refusing to acknowledge Indonesia as a secular state.
For his rigid stand against secularism, Bashir was imprisoned without any trial in 1978. He was held under imprisonment until 1982. Right after his release, he was yet again convicted. He was linked to the bomb attack on Buddhist monument Borobudur in 1985. Evading detention, he fled to Malaysia.
Bashir’s period of exile was somewhat long, until President Suharto’s stint ended in 1998. During this time, he commenced religious teachings in both Malaysia and Singapore, based on Quran and Hadith. He was alleged of developing a close relationship with Jemaah Islamiyah, an alleged militant Islamic group that had close ties with Al Qaeda and Taliban.
Upon returning to Indonesia in 1999, he became a priest and once again called for Sharia Law. During this time, he became the godfather of Jemaah Islamiyah.
He founded and served as a significant member of the group Majelis Mujahidin Indonesia (MMI), a new Islamic organization which aimed at enforcing Islamic Law in Indonesia.
In 2002, the US State Department translator Burks made efforts to take Bashir in charge by insisting President Megawati to secretly hand-over him in a meeting at Megawati's home. However, the latter refused the same.
In 2003, he was formally charged of treason, immigration violations, and providing false documents and statements to the Indonesian police regarding the bombings against Christian churches, which killed 18 people on Christmas Eve in 2000. Found guilty on immigration violation, he was sentenced to three years but was released after 20 months due to his good behavior in the prison.
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He was yet again arrested on October 15, 2004 accused of being involved in the bomb attack on Marriott Hotel in Jakarta in August 2003. Additionally, his involvement in the 2002 Bali bombing that resulted in the death of 202 people was suspected.
In March 2005, he was found guilty of conspiracy behind the 2002 Bali bombings. Resultantly, he was sentenced to two and a half years imprisonment
His period of imprisonment was cut short by 4 months and 15 days by Indonesian government on its Independence Day. Following this, he was released on June 14, 2006. His release was well timed as he published a commemorative book around the same period.
Upon his release, he returned to his boarding school where he served as the spiritual leader. He once again commenced his plans of imposing Sharia Law in Indonesia and even called upon Australian Prime Minister John Howard to convert to Islam else face the wrath of God.
Over the years, he has expressed his sympathy for Osama Bin laden and Saddam Hussein and has been quoted supporting Laden in the latter’s ‘true struggle to uphold Islam’. He instead claimed that America and Israel were ‘true terrorists’ and the 9/11 bombing were a false attack by America and Israel as an excuse to attack Muslims in Afghanistan and Iraq.
In 2006, he publically criticized United Nations for listing him as a terrorist in their list of international terrorists.
In 2008, he announced his intention to start a new Islamic group in Indonesia, JAT or Jamaah Ansharut Tauhid. The launch was made to coincide with the Indonesian government’s preparation of execution of three Bali bombers. Over the years, JAT has been responsible for multiple coordinated attacks against innocent civilians, police and military personnel in Indonesia.
Bashir openly claimed CIA (Central Intelligence Agency) and Israel to be behind the attacks of 2002. He alleged that the CIA officials replaced the bombs by micro-nuclear weapons. He even argued stating that world peace can only be ensured if US stops fighting Islam and instead agrees to be governed by Islam.
In 2010, he was charged of being involved in plans of terror and military training in Aceh by the Indonesian police. In June 2011, he was convicted of supporting a jihadi training camp following a four-month trial. He has been sentenced to 15 years in prison