The idea was to get Mr. Zubair, whose name is Mohd Farik Bin Amin, to testify against Mr. Hambali and another Malaysian, Mohammed Nazir Bin Lep, who is often called Lillie, in exchange for an arrangement to serve his military commissions sentence in a Malaysian prison.
The Malaysians balked and military prosecutors brought charges against Mr. Hambali alone in June 2017. But the office overseeing military commissions never cleared that case for trial. Six months later, prosecutors brought new charges against Mr. Hambali and the two Malaysians. That case was also never approved.
The spokesman for the Office of Military Commissions, Ron Flesvig, was unable to say Wednesday why the prosecutor issued new charges. The Pentagon lawyer with the title of convening authority for military commissions, Melinda L. Perritano, can decide which charges, if any, to approve for trial, Mr. Flesvig said.
The latest charge sheet differs from those brought by prosecutors in December 2017 in one critical respect: It includes the crime of conspiracy in addition to charges of murder in violation of the law of war, terrorism and other war crimes. In a long-running series of appeals, the Pentagon’s Court of Military Commission Review recently declined to consider whether conspiracy was a lawful war crimes charge, leaving intact the 2008 conspiracy conviction of Guantánamo’s lone war crimes convict, Ali Hamza al-Bahlul.
Mr. Bahlul, from Yemen, is serving a life sentence at Guantánamo for making a recruiting video for Al Qaeda and for other activities as Osama bin Laden’s media adviser before the Sept. 11, 2001 terrorist attacks. Mr. Bahlul’s lawyers are appealing that decision at the United States Court of Appeals for the District of Columbia, but prosecutors appear to have been emboldened enough by the Pentagon panel decision to add the charge of conspiracy to the Indonesian bombings case.
Eight of Guantánamo’s 40 prisoners are currently charged with crimes.
In 2012, one of them, Majid Khan, a former C.I.A. black site prisoner, pleaded guilty to delivering $50,000 from Al Qaeda to Jemaah Islamiyah, money that was ultimately used to fund the Marriott bombing in Jakarta, Indonesia. Mr. Khan is scheduled to be sentenced in July.
In a March court filing, his lawyers noted, “Mr. Khan’s ongoing cooperation in another matter, including his possible testimony at trial in that matter.” They did not specify which trial.