Lawyers have scheduled the entry of their pleas for early next year, along with sentencing. Details of the deal were under seal.
Two Malaysian men have reached agreements with military prosecutors at Guantánamo Bay to plead guilty to war crimes charges for being accessories to deadly terrorist attacks in Indonesia two decades ago.
Both men and the lead defendant in the case, Encep Nurjaman, were held for years in the C.I.A.’s secret prison network and transferred to Guantánamo in 2006. They were charged in August 2021, 18 years after they were captured.
Under the deals, the cases of Mohammed Farik Bin Amin, 48, and Mohammed Nazir Bin Lep, 46, have been separated from Mr. Nurjaman’s case.
The two men are accused of having served as money couriers and providing other support to Mr. Nurjaman, an Indonesian man who is known as Hambali, a former leader of the Southeast Asian extremist group Jemaah Islamiyah.
Now he will face trial alone on charges 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 maximum punishment in the case is life in prison.
The military disclosed the existence of the deal this week with the release of a court filing by prosecutors and lawyers for Mr. Bin Amin, which scheduled a hearing starting Jan. 15 for the entry of a plea, assembling a military panel and sentencing. The terms were under seal, including any limits on his prison sentence, where he would serve it and whether his testimony was sought against Mr. Nurjaman.
Less is known about when Mr. Bin Lep will be sentenced. On Thursday, his lawyer, Brian Bouffard, said only that “Mr. Bin Lep will fully cooperate with the U.S. government.” Christine Funk, the lawyer for Mr. Bin Amin, declined to discuss the deal.
But people with knowledge of the agreements said the men were seeking to be sent to a rehabilitation program for Muslim extremists in Malaysia.
None of those with knowledge of the talks were authorized to discuss the arrangements because of the delicacy of the diplomacy involved. Malaysian diplomats visited Guantánamo Bay last month, according to U.S. officials and news reports from Southeast Asia.
The defendants are scheduled to appear at the war court next week for preliminary hearings before the new judge in the case, Lt. Col. Wesley Braun. But no pleas will be taken. The judge has excused Mr. Bouffard and two other lawyers on his team from attending the hearing to travel to Southeast Asia on unspecified business related to the case.
Mr. Nurjaman has a separate hearing next week. His lawyer, James R. Hodes, said he was uncertain of whether or how prosecutors might try to use the pleas of the two Malaysians at his client’s trial.
“These guys should never have been brought to Guantánamo in the first place,” he said. “If they’re admitting to their own guilt and say nothing that implicates Mr. Nurjaman, that’s fine.”
But, he said, any effort by prosecutors to record testimony from the two men and then repatriate them beyond the reach of the court might prejudice or harm his client. Live confrontation is “what our constitution guarantees people accused of crimes,” he said.
Col. George Kraehe, the case prosecutor, did not respond to a request for comment on any aspect of the deal or future trial.
Both Malaysian men reached the agreements with Jeffrey D. Wood, a lawyer and colonel with the Arkansas National Guard who was appointed during the Trump administration as overseer of the war court. He left that job this month and was replaced by a retired Army general, Susan K. Escallier.
Prosecutors and Mr. Wood had been pursuing guilty pleas in the military commissions as a means of closing cases against detainees who were held at secret C.I.A. prisons known as black sites.
Most of those cases have dragged on for more than a decade, in part because of the classified nature of evidence and because lawyers have challenged that evidence as derived from torture.
It will now be up to Ms. Escallier to decide whether to renew talks in the court’s better-known conspiracy case in the Sept. 11, 2001, attacks. Prosecutors recently suspended an effort to settle the case with sentences of life in prison at most, rather than the possibility of capital punishment, after the Biden administration declined to weigh in on the case.
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