A recent court hearing at Guantanamo dealt with national security information so secret that the accused was not even allowed in the room: the first completely closed session of the military commission trials under President Obama.

It was the last day in a week of pre-trial hearings in the case of Abd al Rahim al Nashiri, alleged mastermind of the bombing of the U.S.S. Cole. Government prosecutors had filed a motion that didn’t even have an unclassified title. In a press conference immediately afterward, reporters were told only that it had lasted 78 minutes.

The commission has now released a transcript of the hearing – but one so heavily redacted that divining the focus of the hearing is like filling out crossword puzzle with far too few clues:

But the transcript reveals parts of a lengthy discussion of the CIA’s secret prison program, in which Nashiri was held for four years and subjected to waterboarding and mock executions.

As for what specifically the government asked for in its motion, that’s classified. A government lawyer says only that “the specific nature of the request, the reasons why, and the national security reasons are extremely sensitive.”

The judge’s framing of the problem is also blacked out:

In 2006, Nashiri was transferred to military custody at Gitmo. Nashiri’s lawyers have long argued that his torture and years of confinement outside the law have tainted the capital case against him.

In the transcript, the government says it will turn over information to the defense about Nashiri’s time in CIA custody – including photos of him, relevant portions of legal memos, and summaries of CIA reports:

In response, a defense lawyer says he’s unsatisfied with what the government has given them, but much of his argument is redacted:

He then cites the “real truth,” which is followed by a big, black block:

There have been some officialdisclosures about the black sites, which Obama ordered shuttered upon entering office. But many details of the program remain classified. That limits what Nashiri himself can hear in the case, and what the defense team has access to, even though it has security clearance.

The defense lawyer notes he cannot ask Nashiri about the government’s materials, because so much of it is classified:

(The government prosecutor responds that the defense is “free to discuss” Nashiri’s “recollection” of his treatment. She says, "I am well aware of the facts in this case," and that there are legitimate national security reasons behind any decision to hold back information.)

Reached by ProPublica, the defense lawyer, Rick Kammen, said he could not elaborate at all beyond what was in the transcript.

The judge, James Pohl, had authorized the closed session over the objections of the defense, which claimed that Nashiri’s exclusion from the courtroom that day violated a litany of laws and rights. In arguing that the session needed to be secret, government prosecutors repeatedly pointed to cases in federal court where defendants had been excluded along with the public.

The judge took pains to specify that this was a pre-trial hearing that did not deal with evidence the government planned to use in its main case.

One thing the transcript does make clear is that the same issue – whatever it is – has come up in the trial of the five men accused of plotting the 9/11 attacks. They were also held in CIA custody. Pohl said he would wait to rule until after he hears arguments in that case.