“It’s a courtroom with three benches,” said Eugene R. Fidell, who teaches military justice at Yale Law School. “There’s one person pretending to be the judge, and two other agencies behind the scenes exerting at least as much influence.”

Thirteen years after 9/11, nobody has been convicted in connection with the attacks and, because of the F.B.I. visit, a trial could be delayed even longer. But it was only the latest in a string of strange events at Guantánamo Bay that, coupled with the decade-long delay, have undermined a process that was supposed to move swiftly, without the encumbrances of the civilian legal system and its traditional rules of evidence.

Last year, as a lawyer for Mr. Mohammed was speaking during another hearing, a red light began flashing. Then the videofeed from the courtroom abruptly cut out. The emergency censorship system had been activated. But why? And by whom? The defense lawyer had said nothing classified. And the court officer responsible for protecting state secrets had not triggered the system. Days later, the military judge, Col. James L. Pohl, announced that he had been told that an “original classification authority” — meaning the C.I.A. — was secretly monitoring the proceedings. Unknown to everyone else, the agency had its own button, which the judge swiftly and angrily disconnected.

Last year, the government acknowledged that microphones were hidden inside what looked like smoke detectors in the rooms where detainees met with their lawyers. Those microphones gave officials the ability to eavesdrop on confidential conversations, but the military said it never did so.

“At some point, it just becomes silly,” said Glenn Sulmasy, a military law professor at the Coast Guard Academy who supports military trials for terrorism but said problems at Guantánamo Bay have undermined confidence in the system. “I don’t think we’re at that point yet, but at some point it just becomes surreal. It’s like there’s a shadow trial going on and we’re only finding out about it in bits and pieces.”