Abu Bakar Bashir has been described as the ideological godfather of Jemaah Islamiyah, even though no evidence has been made public that specifically implicates Bashir in terrorist attacks undertaken by the clandestine group. He has claimed that Jemaah Islamiyah doesn't exist and that the Central Intelligence Agency (CIA) and Israel were behind terror attacks in Indonesia including the 2002 Bali bombings After open confessions from the bombers, Bashir claimed in August 2006 that the Bali bombs were "replaced" by a "micro-nuclear" weapon by the CIA. Bashir has expressed sympathy for Osama bin Laden and Saddam Hussein, but that he didn't "agree with all of their actions," in particular "total war." He further stated "...If this occurs in an Islamic country, the fitnah [discord] will be felt by Muslims. But to attack them in their country [America] is fine." He has claimed the 9/11 attacks were a false flag attack by America and Israel as a pretext to attack Muslims in Afghanistan and Iraq.
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 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.
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."