GUANTÁNAMO BAY, Cuba — During a court session this year in the case of the men accused of plotting Sept. 11, defense lawyers spotted something curious: Prosecutors were huddled around a wireless silver tablet computer.
When confronted about it, the judge made a surprising disclosure. He had secretly approved use of the device to allow real-time communication between prosecutors and representatives of the C.I.A. and other intelligence agencies monitoring the trial from afar. The purpose, he said, was to allow the agencies to signal when they were concerned about a potential "spill," the inadvertent disclosure of classified information.
"Spills cannot occur," said the judge, Col. W. Shane Cohen, defending his decision to give the agencies a way to relay requests to silence the court audio. "That is the bottom line. The goal is zero spills."
The judge said he regretted that he had agreed with prosecutors to keep secret the new communication system, but he stood by his decision to allow its use. He released his secret order, calling the wireless silver tablet a "teletype machine."
In granting the request, Colonel Cohen added another layer of secrecy to the at times remarkably opaque national security court at Guantánamo Bay, Cuba.
Government censors black out portions of transcripts of public hearings before they are posted on the military commissions website, which is adorned with the motto, "Fairness Transparency Justice." Witnesses from the prison, including lawyers and some commanders, testify anonymously. Soldiers strip their name tapes off their Army uniforms when on the courtroom premises.
The judge and a court security officer can hit a mute button to silence the audio system that pipes the proceedings — on a 40-second delay — into the sealed-off observation room at the back of the courtroom where relatives of victims, journalists and other visitors watch.
But the secrecy extends beyond the courtroom, which is at the heart of the hybrid federal-military justice system that the United States created in response to the Sept. 11, 2001, attacks that killed nearly 3,000 people.
All court filings, including a judge's order, undergo a security review before the public can see it.
By Defense Department regulation, court filings are to be released to the public within 15 business days. But they undergo a censorship scrub first, with representatives of a series of security agencies like the C.I.A., F.B.I., Guantánamo prison and the Pentagon's United States Southern Command having a say on what portions of the filing are classified.
But delays are common. It took 10 months from filing until the public could read a legal motion from May 2019 asking the Army judge in that case to hold a hearing on the question of granting time served credit for the torture endured by Majid Khan, who pleaded guilty to being a courier for Al Qaeda.
Before Mr. Khan was brought to Guantánamo in 2006, the C.I.A. held him for three years in isolation and incognito in the C.I.A.'s secret prison network, the black sites. There, members of the medical staff "infused" a puréed meal into his rectum after he had gone on a hunger strike, an episode that itself was kept secret at the court until it was included in a declassified portion of a Senate study of the interrogation program.
It is a matter of not only concealing information that is classified — for example the countries that hosted the black sites — but also blacking out words that the intelligence agencies say could create a mosaic of information that could let people discern government secrets. So a continent that was the location of a black site is also classified.
Transcripts of public court sessions are also censored, with at times perplexing results.
On Jan. 27, a defense lawyer questioning James E. Mitchell, the C.I.A. contractor who waterboarded prisoners in 2002 and 2003, read aloud a sentence from Dr. Mitchell's 2016 memoir, "Enhanced Interrogation," which was released with approval of the agency.
In it, Dr. Mitchell, a psychologist, described the staffing of a black site this way: "There were also computer and communications geeks, analysts, targeters, subject matter experts, many, many agency police officers to act as security guards, two psychologists (counting me), nurses, and a physician."
The transcript, released two weeks later, blacked out the words "agency police," as though the C.I.A. had, on reconsideration, not wanted the world to know it used its own police force in the clandestine prison system.
"The commissions are susceptible to it because they are captive to the agency," said Joshua L. Dratel, a New York criminal defense lawyer who has handled dozens of federal national security cases and represented David Hicks, a prisoner at Guantánamo who went home to Australia in 2007 as part of plea deal in a conviction that was overturned in 2015.
Mr. Dratel returned to the war court in February as an observer for the American Bar Association and spotted the court's motto sewn into a carpet at the entrance.
"You looking at the floor, there's a rug that says 'blah, blah, blah transparency, and then you look up and you see a soldier in front of you, another one, and they have their names taped over," he said. "To me it's just the dissonance of Gitmo."
In federal court in the United States, a defendant can choose to testify and tell his or her own story and let a judge or jury decide the truth of it. But at Guantánamo, Mr. Dratel said, even the detainee's own story can be classified.
Lawyers for the man accused of plotting the Sept. 11 attacks, Khalid Shaikh Mohammed, are forbidden from releasing the full details of his memories of his interrogations — he was waterboarded 183 times — because where they were done, and the identities of some of those who he believes carried them out, are classified.
Defense lawyers in the Sept. 11 case were particularly outraged over the decision by Colonel Cohen, who abruptly announced in recent days that he was stepping down as the trial judge, to secretly allow prosecutors a direct channel of communication with the intelligence agencies from inside the court.
In 2013, the C.I.A., which was monitoring the proceedings from outside the courtroom, used the ability it had at the time to remotely mute the audio at a mention of the intelligence agency's secret prison network.
The judge at that time, Col. James L. Pohl, was furious. He ordered anybody with remote access to the court's systems to unplug. Colonel Cohen's decision to allow the intelligence agencies to communicate directly with prosecutors in the courtroom during the proceedings effectively restored that ability, albeit through a prosecutor who was reading warnings from the C.I.A. somewhere else and signaling the court security officer to cut the feed.
Retroactive redaction is not unusual at the court. In last year's motion in the Khan case, censors twice blacked out the name of President George W. Bush in an Amnesty International report from 2007 that recounted public remarks Mr. Bush had made in 2006.
The rule-making can be random and constantly changes. In January, students, lawyers and human rights advocates who were at Guantánamo to observe a hearing were instructed that they were forbidden to talk about the Sept. 11 case outside the confines of Camp Justice, the crude housing area of tents and trailers at the razor-wire ringed court complex.
Julia Hall, who works for Amnesty International, said she was discussing the case with other observers at O'Kelly's, the base's Irish pub, when a chaperone waved her hand in front of her mouth to silence her. The gag order was rescinded the next day.
A new delegation of observers brought to the base the next week were given a new gag order: They were forbidden to talk about how many soldiers were inside the court guarding the defendants.