Experts say a full trial would be risky and embarrassing for the US, as much of the evidence against him is likely to have been made under duress. While the military court may attempt to avoid a full trial by seeking a plea deal in which he agrees to return to Indonesia, analysts said this could also prove problematic as Indonesia may refuse to take him given his continuing influence.

In addition to the Bali bombing, which killed 11 Hong Kong residents among its scores of victims, Hambali is alleged to have been behind the 2003 attack at Jakarta’s JW Marriott hotel that killed 11.

Professor Zachary Abuza, of the National War College of Washington, said a full trial was likely to be “very bad for the US government”.

It would also be compromised by the nature of the evidence against Hambali and his associates and their treatment in Guantanamo, Abuza said. “At best, they were held indefinitely without charge, their confessions made under duress, and many were tortured,” he said.

“Military prosecutors tried to find sufficient open source evidence that did not come from enhanced interrogations to lead to his conviction. They could not,” added Abuza, who specialises in terrorism.

Abuza said that after Hambali’s capture in Thailand in 2003 he had been kept in secret CIA black sites, before being transferred along with other senior al-Qaeda operatives to Guantanamo Bay in 2006.

“It’s in the US government’s interest to reach a plea bargain, without a trial,” said Abuza. “[A trial] could be very bad for the US government. Many were tortured, all have been detained for nearly 20 years without charge; these are affronts to the rule of law,” said Abuza.

Abuza said in similar cases, what had happened was that detainees admitted guilt, were sentenced to time already served, then returned to their home country, where they were either jailed or released. But this would depend on Indonesia agreeing to take him back – an assumption that is far from certain.

My brother, the ‘Osama bin Laden of Southeast Asia’

“Any part of a plea agreement has to be coordinated with the defendant’s home country,” said Abuza, adding that if Indonesia refused to take Hambali back, the US “really has nothing to offer the defendant in the plea agreement”.

A senior security source in Jakarta said there had been “no communication from the US with regards to the upcoming trial”.

Abuza said the Indonesian government was “clearly fearful of having him returned to Indonesia” where he could be treated by militants as a martyr.

“The Indonesians are working so hard to deal with the threat posed by militants, the last thing they want to do is allow an inspirational figure to return to the country. Their counterterrorism forces are very good but are already spread thin,” said Abuza.

He said the headache now facing the US was a result of its “terrible mistake” in not immediately putting al-Qaeda suspects on trial in the US federal court system, which has a long and successful record in securing terrorist convictions.

“The overarching goal of the US government is not necessarily to put these people on trial – that ship has long sailed – but to close down Guantanamo Bay,” Abuza said.

An inspiring figure

“Hambali is seen as someone who suffered and survived Guantanamo Bay and this inspires awe in jihadis,” said Nasir who left Jemaah Islamiah in 2003 and is now involved in deradicalisation efforts.

He said Hambali’s past in Afghanistan, where he had trained in the Mujahideen Military Academy in the late 1980s, added to his legend.

US authorities allege that Hambali went to fight the Russian occupation in Afghanistan in 1987 and met Osama bin Laden, the mastermind of the September 11 attacks on New York and Washington.

Jihadis have now glorified Hambali, said Nasir, adding that in person the alleged terrorist mastermind came across as friendly and willing to help others, mindful of his words and always polite.

“Hence he is liked by many people. If one does not have critical thinking, it is easy to be swayed by the wave of his thinking,” said Nasir.

“As an inspiring figure, unless he changes his attitude or expresses words of regret and repentance, there will be worries over accepting Hambali back in Indonesia,” said Nasir.

However, he said that were Hambali to express regret and call on others “to stop acts of terrorism” he could have a “positive impact”.