A Guantánamo 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 Bin 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 Mr. Bin Amin had agreed to testify against his co-defendants, what sentence he would receive and where he would serve it. Christine Funk, a defense lawyer for Mr. Bin Amin, and Col. George Kraehe, a prosecutor on the case, each declined to comment.
Late in the Obama administration, the government nearly struck a plea deal with Mr. Bin 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 recognize the tribunals system as legitimate.
A conviction of Mr. Bin 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 C.I.A. prisons known as black sites. Such cases are complicated by the fact that the agency tortured the prisoners before transferring them to military custody, and by the heavy presence of classified information.
No former C.I.A. 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 United States Embassies in East Africa. But Congress has banned bringing any more Guantánamo detainees to the United States for trials in federal court.
In 2012, another former C.I.A. detainee, Majid Shoukat Khan, pleaded guilty before a military commission at Guantánamo; he was freed in Belize earlier this year. Last year, another such detainee, Abd al-Hadi al-Iraqi, pleaded guilty before a commission and is expected to be sentenced next year.
The flagship cases before the military tribunal at Guantánamo have been bogged down in pretrial proceedings for more than a decade. Those include five former C.I.A. detainees accused of aiding the terrorist attacks of Sept. 11, 2001, and a former C.I.A. detainee accused of conspiring in the bombing of the American 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 C.I.A. program released by the Senate Intelligence Committee in December 2014 cited Mr. Bin Amin’s case as an example of C.I.A. interrogators going beyond authorized techniques.
In one episode, an interrogator placed a broomstick behind Mr. Bin 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 C.I.A. also held the other two co-defendants in the case, Encep Nurjaman, who is known as Hambali, and Mohammed Nazir Bin Lep, sometimes called Lillie.
Prosecutors believe the three men were members of Jemaah Islamiyah, a militant Islamist group in Southeast Asia. They portrayed Mr. Nurjaman as the mastermind of the bombings and Mr. Bin Lep as his key lieutenant. Mr. Bin Amin has been portrayed more as a bagman who is believed to have helped Mr. 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 C.I.A. prison network. The U.S. 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 Mr. Bin Amin failed, military prosecutors continued to work on the case, including notifying Mr. Nurjaman in 2017 that they had proposed charges against him.
A Trump administration appointee who oversees the commissions system, Jeffrey D. Wood, 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 Mr. Bin Amin to separate his case, is set to step down on Oct. 8.