Something Classified Was Scheduled at Guantánamo. A Judge Stopped It.

Mohammed Nazir Bin Lep, in a photo provided by his lawyers, at Guantánamo Bay. United States, 2019.

Mohammed Nazir Bin Lep, in a photo provided by his lawyers, at Guantánamo Bay. United States, 2019.

GUANTÁNAMO BAY, Cuba — Something secret was supposed to start on Saturday related to the case of a Malaysian prisoner who has been held as a terror suspect for 13 years at Guantánamo Bay.

Then a federal judge put a stop to it following a classified hearing. The judge did not say what it was or why he had blocked it, other than to note that he was making his order public so that the people involved did not arrive for the secret proceeding only to find that it had been canceled.

“The defendants are restrained from conducting the two proceedings that are scheduled to commence on September 28, 2019, in a certain location,” Judge John D. Bates of the U.S. District Court in Washington, D.C., wrote in an order dated last Friday but released this week. “We are issuing this order today as a courtesy to petitioner and defendants as it may affect their travel or logistical arrangements.”

Judge Bates’s reasoning for issuing the order is classified, as were all the associated filings, including an emergency habeas corpus petition filed by military and civilian lawyers for the defendant, Mohammed Nazir Bin Lep.

But people with general knowledge of what was to take place said military commission prosecutors and defense lawyers for Mr. Bin Lep and two other Southeast Asian men had Defense Department approval to travel to both an undisclosed overseas location as well as Guantánamo to carry out the mysterious proceedings.

Mr. Bin Lep, 42, is a Malaysian man whom the United States intelligence community considers a lieutenant to an Indonesian prisoner known as Hambali, 55, who is in turn described as “an operational mastermind” of the Southeast Asian extremist group Jemaah Islamiyah. United States and Thai security forces captured Mr. Hambali, Mr. Bin Lep and another Malaysian man, Mohd Farik Bin Amin, 44, in 2003. They spent three years in the secret overseas prison network of the C.I.A. before they were transferred to Guantánamo Bay prison in 2006.

Pentagon prosecutors have repeatedly tried, and failed, to charge Mr. Hambali, Mr. Bin Lep and Mr. Bin Amin since 2017. Three successive overseers of the military commissions, people who hold the title of convening authority, have refused to approve the case. In the meantime, the three men are held as Law of War prisoners, essentially irregular P.O.W.s in the war on terror.

Two people with knowledge of the case said there was an effort to take sworn statements in the case but would not say on whose authority, since there is no judge. The Manual for Military Commissions allows for the convening authority to authorize depositions. Retired Rear Adm. Christian Reismeier, the current convening authority, had no comment, said Ron Flesvig, the spokesman for the Office of Military Commissions.

Last Friday night, after Judge Bates issued his order, the Office of Military Commissions halted plans to airlift a team of court stenographers and lawyers who were assigned to the case to Guantánamo the next morning.

A lawyer for Mr. Bin Amin, Lt. Col. Chantell Higgins of the Marines, declined to comment on what was to take place. She was reached by telephone in Kuala Lumpur, the capital of Malaysia where, she said, she was conducting a routine investigation as part of her defense duties for Mr. Bin Amin.