This article was produced in partnership with the Pulitzer Center on Crisis Reporting.

GUANTÁNAMO BAY, Cuba — On a Monday morning four and a half years ago, Ramzi bin al-Shibh, one of the men accused of conspiring in the Sept. 11 attacks, made a stunning announcement for all in the military courtroom to hear: He knew the new Arabic translator sitting beside him from the secret C.I.A. prison network where the United States tortured its detainees.

What followed said a lot about the enduring secrecy around the torture program and the black-site prisons, the disputes over what evidence is admissible in the war court established to try terrorism suspects and the grindingly slow effort to get justice in the 2001 attacks.

By blurting out the man’s name in open court, Mr. bin al-Shibh had undercut the government’s efforts to keep under wraps the identities of most people who worked at the black sites. The interpreter’s name, initially included in the court transcript for that day, was later redacted. Defense lawyers were instructed — in secret — that what happened was a security breach and that they were forbidden, by a national security directive, to publicly acknowledge what had happened in open court.

Never mind that the interpreter’s name was called out publicly at the Guantánamo air terminal at the end of that week as lawyers and journalists checked in for their flight back to the United States.