He runs the Al-Mukmin boarding school in Ngruki, Central Java which he co-founded with Abdullah Sungkar in 1972. He was in exile in Malaysia for 17 years during the secular New Order administration of the President of Indonesia Suharto resulting from various activities, including urging the implementation of Sharia law.
Intelligence agencies claim he is the spiritual head of Jemaah Islamiyah (also known as JI) and has links with Al-Qaeda. Bashir, however, denies connections with Jemaah Islamiyah or terrorism stating he does not believe Jemaah Islamiyah exists.
In 1972, Bashir founded Al-Mukmin boarding school with friends Abdullah Sungkar, Yoyo Roswadi, Abdul Qohar H. Daeng Matase and Abdllah Baraja. Al-Mukmin is located in Ngruki, near Solo, Central Java. Initially, Al-Mukmin's activities were limited to religious discussion after only short Islamic forum after dhuhr (mid-day prayer). Following increasing interest, the founders expanded Al-Mukmin into Madrasah (Islamic school) and then to Pesantren (Islamic boarding school).
During President of Indonesia Suharto's New Order, Bashir and Sungkar were arrested for a number of reasons, firstly for actively supporting Sharia, the non-recognition of the Indonesian national ideology Pancasila which in part promotes religious pluralism. Secondly, the refusal of their school to salute the Indonesian flag which signified Bashir's continual refusal to recognise the authroity of a secular Indonesian state. Bashir appealed but was subsequently imprisoned without trial from 1978 to 1982 . Soon after his release, Bashir was convicted on similar charges; he was also linked to the bomb attack on the Buddhist monument Borobudur in 1985 but fled to Malaysia. During his years in exile Bashir undertook religious teachings in both Malaysia andSingapore. USA alleged that during this period he became involved with Jamaah Islamiyah, an alleged militant Islamist group. Bashir remained in exile until Indonesian President Suharto's fall in 1998 . Bashir returned to Indonesia in 1999 and became a leading cleric, renewing his call for Sharia law.
"There is no nobler life than to die as a martyr for jihad. None. The highest deed in Islam is Jihad. If we commit to Jihad, we can neglect other deeds, even fasting and prayer".Abu Bakar Ba’asyir, Jakarta 2005
Controversy surrounding Abul Bakar Bashir heightened in early 2008 after a sermon given by the cleric in late 2007. Bashir allegedly refers to tourists in Bali as 'worms, snakes and maggots' with specific reference to the immorality of Australian infidels.. Bashir states
the young must be first at the front line, don't hide at the back. You must be at the front, dies as martyrs and all your sins will be forgiven. This is how to achieve forgiveness...'. As described by Natasha Robinson, Bashir has returned to his hardline rhetoric. His early release from prison has been described as the catalyst to his revitalised, hardline approach towards non-Muslims. Bashir's view on non-Muslims is highlighted in this statement made in East Java in 2006, 'God willing, there are none here, if there were infidels here, just beat them up.Do not tolerate them.'. Bashir's specific mention of Australian tourists has created uproar among Government officials and the Australian media regarding the cleric's so called intolerant comments. Australia's Foreign Affairs Minister Stephen Smith views Bashir's comments in late 2007 as being full of the intolerance that has marked many of Bashir's previous speeches.
The cleric has also previously warned of severe retribution if the Bali bombers, who killed 202 people in 2002, be executed by firing squad. On 24 March 2008 the Bali bombers, who are on death row, lost almost any hope of escaping the death penalty as their lawyer, Fahmi Bachmid, withdrew from their last appeal.. The process of execution is likely to start sooner than expected, indeed bringing Bashir's previous comments regarding the Bali bombers' fate to attention.
On April 14, 2003, he was formally charged by the Indonesian government with treason, immigration violations, and providing false documents and statements to the Indonesian police. The charges are mainly related to the 2000 Christmas Eve bombings against Christian churches, which killed 18 people. In the Indonesian court, he was found not guilty of treason because the state failed to prove its case, but was found guilty on the immigration violations. In a local TV news interview, Metro TV, when asked, 'Are you truly a terrorist?'; He simply answered, 'No, I've never killed anyone.' He was sentenced to three years in prison, but the sentence was subsequently reduced to 20 months due to his good behavior in the prison.
On October 15, 2004, he was arrested by the Indonesian authorities and charged with involvement in the bomb attack on the Marriott Hotel in Jakarta on August 5, 2003, which killed 14 people. Secondary charges in the same indictment accuse him of involvement in the 2002 Bali bombing, the first time he has faced charges in relation to that attack which killed 202 people. On March 3, 2005, Bashir was found guilty of conspiracy over the 2002 attacks, but was found not guilty of the charges surrounding the 2003 bombing. He was sentenced to two and a half years imprisonment.
After returning to the boarding school for which he is the spiritual leader, he pledged a renewed campaign to impose Islamic sharia law on Indonesia. He also called Australian Prime Minister, John Howard, to convert to Islam in order to save him from hell and receive God's forgiveness. Howard said that Australians would be "extremely disappointed, even distressed" at the news of the release. In August 2006, Bashir claimed that the 2002 Bali bombs were replaced by the American CIA with a "micro-nuclear" weapon. He also claimed the original bombs were only intended to injure people, not kill them - despite the bombers' own admissions and public testimony. In answer to one reporter's question as to what the West and the United States can do to make the world safer, Bashir replied, "They have to stop fighting Islam. That's impossible because it is sunnatullah [destiny, a law of nature], as Allah has said in the Koran. If they want to have peace, they have to accept to be governed by Islam."
On December 21, 2006, Bashir's conviction was overturned by Indonesia's Supreme Court. He publicly criticised the United Nations because he remained on the body's list of international terrorists, saying "I am terrorist number 35 on the list.