WASHINGTON – A Guantanamo detainee accused of being an accessory to deadly terrorist attacks in Indonesia two decades ago has severed his military commission case from that of his two co-defendants, a move that suggested a plea deal could be in the works.

The detainee, a Malaysian man named Mohammed Farik Amin, is no longer being tried with two other suspects in the case, according to a court filing posted this week.

They are accused of murder, terrorism and conspiracy in the 2002 bombings of nightclubs in Bali that killed 202 people and the 2003 Marriott hotel bombing in Jakarta that killed 11 people.

The court filing did not say whether a plea deal had been reached, and if so, whether Amin had agreed to testify against his co-defendants, what sentence he would receive and where he would serve it.

Ms Christine Funk, a defence lawyer for Amin, and Colonel George Kraehe, a prosecutor on the case, each declined to comment.

Late in the Obama administration, the government nearly struck a plea deal with Amin in which he would have been repatriated to Malaysia to serve out most of his sentence.

But the deal collapsed amid concerns that he would not remain imprisoned for the full term, in part because Malaysia might not recognise the tribunals system as legitimate.

A conviction of Amin through a guilty plea would fit a strategy at the military commissions system of trying to use that approach to resolve charges against detainees formerly held at secret Central Intelligence Agency (CIA) prisons known as black sites.

Such cases are complicated by the fact that the agency tortured prisoners before transferring them to military custody, and by the heavy presence of classified information.

No former CIA detainee has been convicted at trial before a military commission, although one – Ahmed Khalfan Ghailani – was brought to the United States for a civilian trial, convicted in a mixed verdict, and sentenced to life in prison in 2011 for his role in the 1998 bombings of two US embassies in East Africa. But Congress has banned bringing any more Guantanamo detainees to the US for trials in federal court.

In 2012, Majid Shoukat Khan, another former CIA detainee, pleaded guilty before a military commission at Guantanamo; he was freed in Belize in 2023.

In 2022, another such detainee, Abd al-Hadi al-Iraqi, pleaded guilty before a commission and is expected to be sentenced in 2024.

The flagship cases before the military tribunal at Guantanamo have been bogged down in pretrial proceedings for more than a decade.

Those include five former CIA detainees accused of aiding the terrorist attacks of Sept 11, 2001, and a former CIA detainee accused of conspiring in the bombing of the US destroyer Cole off the coast of Yemen in October 2000.

In March 2022, prosecutors in the Sept 11 case invited lawyers for the defendants to negotiate over a potential plea deal that would have made the maximum punishment life in prison rather than death.

The defendants made certain demands, and prosecutors have been waiting over a year for the Biden administration to weigh in.

A study of the CIA programme released by the Senate Intelligence Committee in December 2014 cited Amin’s case as an example of CIA interrogators going beyond authorised techniques.

In one episode, an interrogator placed a broomstick behind Amin’s knees when he was being forced to stay in a stress position. Stress positions had been approved for him, the report said, but the use of the broom to heighten the pain was not.

The CIA also held the other two co-defendants in the case – Encep Nurjaman, who is known as Hambali, and Mohammed Nazir Lep, sometimes called Lillie.

Prosecutors believe the three men were members of Jemaah Islamiah, a militant Islamist group in South-east Asia.

They portrayed Nurjaman as the mastermind of the bombings and Lep as his key lieutenant. Amin has been portrayed more as a bagman who is believed to have helped Nurjaman evade arrest after the Bali bombings and who moved funds later used to finance the attack in Jakarta.

The defendants were captured in Thailand in 2003 and spent more than three years in the secret CIA prison network.

The US government deemed the 2002 and 2003 attacks to be war crimes that were carried out by an affiliate of Al-Qaeda, making them eligible for trial by a military commission.

After the earlier negotiations over a plea deal for Amin failed, military prosecutors continued to work on the case, including notifying Nurjaman in 2017 that they had proposed charges against him.

Mr Jeffrey Wood, a Trump administration appointee who oversees the commissions system, approved moving forward with a case against all three on the second day of the Biden administration.

They were arraigned in August 2021, and prosecutors have proposed holding a trial in 2025. Mr Wood, who approved allowing Amin to separate his case, is set to step down Oct 8. NYTIMES