A defense lawyer was making a constitutional argument in the Guantánamo war court that the clock had run out on a case involving terrorist attacks in Indonesia 20 years ago when he was suddenly drowned out by white noise.

“It is repugnant …” were the last words the public heard from Lt. Ryan P. Hirschler, a military lawyer on the defense team.

Spectators watched through soundproof glass while lawyers huddled in confusion over what caused a court security officer to silence the lawyer midsentence. Once the audio was restored, the judge cautioned Lieutenant Hirschler to stick to legal principles and avoid the facts surrounding the case of Encep Nurjaman, an Indonesian man who is better known as Hambali, and two co-defendants.

Even without a fuller explanation, however, the episode helps show why justice comes so slowly at Guantánamo Bay.

More than 20 years have elapsed since the attacks in Bali and Jakarta killed more than 200 people, seven of them Americans. The three men have been in U.S. custody for nearly two decades, starting in C.I.A. prisons. But the lawyers and judge are still trying to figure out what portions of the proceedings are supposed to be secret.

Secrecy permeates the proceedings like no other American court.

The public hears the audio on a 40-second delay. It is enough time for prosecutors to signal to a court security officer, who is schooled in C.I.A. secrets, to press the “security classification button.” More colloquially, it is known as “the censorship switch.” A red light then goes off on a device on the judge’s bench that looks like one used in a hockey game to signal a team has scored a goal.

What constitutes a secret can be perplexing at the special court, which was created after the Sept. 11, 2001, attacks to try foreign suspects in the war on terror. For a time in other long-running cases, the mere mention of the C.I.A. or the word “torture” triggered it. Those are no longer taboo.

Mr. Hambali’s lead lawyer, James R. Hodes, was not permitted to explain what the junior lawyer on his team said after “repugnant.”

“It’s ridiculous, it’s frustrating and it’s nonsensical,” he said. “When the buzzer went off, I said, ‘You’ve got to be kidding me.’”

Those privy to classified information say the secrets at the war court generally center on the years the defendants were held by the C.I.A. and tortured. Sometimes these are the identities of people who worked in the program or facts about other intelligence agencies that operated there. Sometimes it is information that was made public long ago, often in news reports, but that is still officially classified.

In the Sept. 11 and U.S.S. Cole cases, witnesses, lawyers, even the judge are obliged to refer to a country where the C.I.A. held its prized prisoners in 2003 as “Location 4.” But in 2021, as the U.S. Supreme Court heard arguments in a states secrets case brought by a Guantánamo prisoner known as Abu Zubaydah, the justices repeatedly named the place: Poland.

Some information about the Guantánamo prison is also unmentionable in open court — including the location of Camp 7, where former C.I.A. captives, including the men in the so-called Bali bombing case, were held from 2006 to 2021, the identities of people who worked there and a surveillance system of detainees’ conversations in their recreation yards.

Lieutenant Hirschler was arguing that the case should be dismissed because the defendants were not brought before a court sooner. A day earlier, prosecutors had proposed the trial start in March 2025, in part to give them enough time to process classified evidence.

“For 18 years, the government sat on this case,” the defense lawyer said. The three defendants were captured in Thailand in 2003 and transferred to Guantánamo Bay with other men held by the C.I.A. as high-value prisoners in September 2006, one reason Congress enacted the military commissions later that year.

Prosecutors have been building their case against Mr. Hambali and the others since at least 2016. Then, in a failed effort, they tried to get one defendant, Mohammed Farik Bin Amin, to plead guilty and testify against the others. But Mr. Hambali and his co-defendants were brought before a court for the first time in August 2021, for an arraignment that was delayed a few months by the pandemic. Lieutenant Hirschler was arguing in April at only their second court appearance.

The judge, Capt. Hayes C. Larsen, has yet to rule. He said in court that the speedy trial question presented “interesting legal issues as it relates to the interplay between the various laws that have been cited by the parties.”

He asked when, in the prosecutor’s view, did the United States begin its criminal investigation of Mr. Hambali and his two Malaysian co-defendants — and the security officer cut the sound to the public.

The audio was restored six minutes later. The judge said that there was “an issue” and it “has now been addressed.”