When a jury of military officers is assembled this week at Guantánamo Bay, it will be asked to choose a sentence in the 20- to 25-year range for two Malaysian prisoners who admitted to conspiring with an affiliate of Al Qaeda that carried out a deadly bombing in Indonesia two decades ago.

But behind the scenes, through a secret agreement that was negotiated with a senior Trump-era official, the men could be returned to Malaysia before the end of the year.

The sentencing proceedings for Mohammed Farik Bin Amin, 48, and Mohammed Nazir Bin Lep, 47, are part of a U.S. government strategy of trying to resolve Guantánamo’s national security cases through plea negotiations. The men spent years in secret C.I.A. prisons following their capture in 2003. In reaching the agreement, prosecutors averted lengthy litigation over torture that has stymied two capital cases, the Sept. 11 attacks and the bombing of the U.S.S. Cole.

The two men were captured along with a onetime member of the Qaeda affiliate, an Indonesian known as Hambali.

Last week they pleaded guilty to conspiring in a pair of suicide bombings on the resort island of Bali that killed 202 people on Oct. 12, 2002. As part of the plea agreement, they were questioned by prosecutors on Sunday and Monday, potentially for use in the trial of Mr. Hambali, which prosecutors want to hold next year.

The testimony is secret for now. But in their plea they said they had no firsthand knowledge that Mr. Hambali was responsible for the attack. They said they learned afterward from news reports on the internet that Mr. Hambali was wanted for a string of attacks carried out by the Jemaah Islamiyah movement and that they helped him elude capture.

A portion of the plea agreement that envisions their return to Malaysia is also secret.

The judge, Lt. Col. Wesley A. Braun, announced in court that the plea agreement limited the jury to deciding a sentence of no less than 20 and no more than 25 years. He did not disclose whether the sentence could be reduced as part of the cooperation agreement.

But the judge cited an unusual exception to a requirement that they waive all appeals of their convictions. If they are still at Guantánamo 180 days after a senior Pentagon official approves the sentence, they can petition a federal court for their release.

Separately, Colonel Braun has also awarded the defendants some undisclosed sentencing credit for the prosecution’s failure to give defense lawyers evidence in a timely manner, according to legal staff who have seen the ruling. It has not been made public.

The plea agreement was reached by Jeffrey D. Wood, who served as the war court overseer, or Convening Authority, from April 2020 until about three months ago. His successor, Susan K. Escallier, will evaluate whether the Malaysian men cooperated fully with the government and whether any promises Mr. Wood made about a shortened sentence must be fulfilled.

The process is complicated. In the hybrid military-civilian court that President George W. Bush built after the Sept. 11 attacks, the overseer has the power to reduce a prisoner’s sentence but not to order a detainee’s release. A federal court judge can do that, but then the State Department would have to negotiate an agreement to transfer the detainee to another country that satisfies any security concerns of the defense secretary.

So there is no imminent prospect of a plane whisking the men home — even if to Malaysia’s respected rehabilitation center for recovering jihadists.

In their written guilty plea, the men admitted to going to Afghanistan in June 2000. There, they trained in a Qaeda camp on “basic military tactics, topography and firearms,” including how to fire assault rifles and rocket propelled grenades.

In late 2001, Mr. Hambali arranged for them to meet with Osama bin Laden, according to the agreement. They swore an oath of allegiance to him and agreed to become suicide bombers in an operation that was later canceled. The trainees traveled to Thailand in December 2001 and agreed to help Mr. Hambali elude capture. They also conducted surveillance of an Israel airline counter in Bangkok and obtained weapons and false passports, and at least one of them collected cash from a Qaeda courier from Pakistan.

What this means for Mr. Hambali is unclear. James R. Hodes, his lawyer, has said that he is awaiting evidence from the government to prepare for trial. Some of the most sensitive and secret information involves what C.I.A. agents did to detainees in an overseas prison network, where waterboarding, sleep deprivation, beatings and other abuses were part of a program of now outlawed “enhanced interrogation” techniques.

In 2003, according to a Senate study of the C.I.A. program, an interrogator told Mr. Hambali that he would never go to court because “we can never let the world know what I have done to you.” That study was released in 2014, and whatever the interrogator did to Mr. Hambali has not been disclosed.

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