WASHINGTON—Seven years ago, when a former C.I.A. prisoner, Majid Khan, pleaded guilty at Guantánamo to being a courier for Al Qaeda, his lawyers were warned that any mention of the word "torture" would lead a court security officer to trigger a mute button so the public, listening on a 40-second delay, would not hear it.
This week the question of his treatment was front and center, this time in a pre-sentencing hearing. Mr. Khan's lawyers asked a military judge on Monday to order prosecutors to produce evidence and witnesses about the secret prison network where the intelligence agency kept Mr. Khan incommunicado from March 2003 to September 2006.
"The material we seek, that is uniquely in the possession of the government, concerns Mr. Khan's torture," one of his lawyers, Katya Jestin, told the judge. "The C.I.A. torture program in this case, your honor, appears to be the third rail."
No security officer hit the mute button. A red light on the judge's bench used to signal a security breach never lit up.
17-and-a-half years after the September 11, 2001, terror attacks, and a decade after President Barack Obama ordered the C.I.A. to dismantle any remnants of its global prison network, the military commission system is still wrestling with how to handle evidence of what the United States did to the Qaeda suspects it held at C.I.A. black sites. While the topic of torture can now be discussed in open court, there is still a dispute about how evidence of it can be gathered and used in the proceedings at Guantánamo Bay, Cuba.
By law, prosecutors cannot use evidence gained through torture—or any other involuntary statements—at the war court, where eight of Guantánamo's 40 prisoners are accused of being complicit in terrorist attacks. Prosecutors have made clear that nothing the defendants said at the black sites will be used as evidence.
But defense lawyers have continued to press for details of what happened to their clients and to be able to use the information either to fight the charges or to win more lenient sentencing. And they have been aided by changing circumstances, not least the government's declassification of some details of how the prisoners were interrogated by the C.I.A.
The issue has been most intensely debated in Guantánamo's two death-penalty cases: the 9/11 terror attacks that killed 2,976 people and the bombing of the USS Cole in 2000 in which 17 American sailors died.
Defense lawyers in those cases have sought for years to get access to eyewitnesses and graphic details from the C.I.A. sites. The lawyers want to use descriptions of torture to ask the judge to exclude some of the defendant's own statements after they left the black sites. The defense lawyers also have said they would cite torture to seek dismissal of the charges on grounds of outrageous government conduct, an extraordinary legal defense that is used in civilian courts but is seldom granted.
If the men are convicted, the lawyers want the details of how the defendants were treated to argue that the United States has lost the moral authority to execute men it has tortured.
The fight over access to evidence and witnesses from the black sites is one of the factors that has slowed progress in the cases. In the process, it has illustrated how fundamental legal issues about the rights of Guantánamo defendants remain unresolved—and how the passage of time is altering how some of them are handled.
The conflict is not limited to the death penalty cases, as Mr. Khan's proceedings show.
The topic of his torture was strictly taboo on February 29, 2012, when he made his first court appearance since disappearing from his native Pakistan in 2003 at age 23. At that first hearing, Mr. Khan, who lived in suburban Baltimore for seven years and graduated from high school there in 1999, admitted to volunteering to work for Al Qaeda after September 11 and plotting with Khalid Shaikh Mohammed, the accused architect of the attacks.
But in the intervening years, the Obama administration declassified details of what Mr. Khan said the C.I.A. did to him. By his account, he was beaten, hung naked from a wooden beam for three days with no food, kept for months in darkness, and submerged, shackled and hooded, into a tub of ice and water.
Additional details of his treatment were revealed in the partly declassified introduction to a Senate study of the George W. Bush administration's black site program. In his second year of C.I.A. detention, according to a cable cited in the study, the agency "infused" a purée of pasta, sauce, nuts, raisins and hummus up Mr. Khan's rectum, because he went on a hunger strike.
The C.I.A. calls this "rectal feeding." Defense lawyers call it rape.
Mr. Khan's lawyers now want to call witnesses and gather evidence to show his sentencing jury what happened to him.
The litigation over black site evidence has gone on for years, to the dismay of some family members who lost loved ones to Al Qaeda terrorists, particularly families of those killed on September 11, 2001, when hijackers crashed four passenger planes into the World Trade Center, the Pentagon and a Pennsylvania field.
"What our family members endured during the attacks on the airplanes and in the building was beyond torture," said Terry Strada, whose husband Thomas was killed in the World Trade Center.
She has campaigned for more transparency about what happened on September 11. But she sees the focus in the Guantánamo hearings on what happened to the defendants in the black sites as "stalling and stonewalling the process."
In Mr. Khan's case, he has pleaded guilty to delivering $50,000 of Qaeda money to a Southeast Asian affiliate that was used to finance the bombing of a Marriott hotel in Jakarta, Indonesia, in 2003 that killed 11 people. He also admitted to agreeing to assassinate Pervez Musharraf, then the president of Pakistan, a plot that was never pulled off.
Under a plea agreement, he became what his military attorney, Lt. Cmdr. Jared Hernandez of the Navy, called "Guantánamo's sole high-value cooperator" and can be sentenced to 25 years confinement. He is being credited with time served since his plea deal, meaning he could get out in 2037.
His lawyers say testimony about his years in C.I.A. custody could strengthen a post-sentencing clemency petition. They also may ask the judge to grant him credit for those years in the C.I.A. prisons as pretrial punishment and reduce his sentence.
In the military tribunal system, prosecutors are the gatekeepers of classified trial evidence. They have forbidden defense team members from independently contacting or investigating most former black site workers. The C.I.A. is shielding their identities as well as the nations that hosted the black sites, invoking national security, though most if not all the nations have already been identified publicly.
"The C.I.A. is not on trial," Jeffrey Groharing, a case prosecutor, told the judge at a hearing at Guantánamo on Nov. 15. That same day, in a bid to persuade the judge that the prosecution had met its responsibility to provide information to the defense, Mr. Groharing stood at the war court and read aloud from documents the defense lawyers can use from a C.I.A. inspector general's investigation.
One described how, during an interrogation, Mr. Mohammed refused an interrogator's order to drink water. According to the document read by Mr. Groharing, Mr. Mohammed "was taken back to the bathing room, placed on a plastic sheet and a medical officer rehydrated Mohammed rectally. Mohammed clearly hated the procedure. When he was returned to the interrogation room, he then complied and drank water."
In another document Mr. Groharing read, an unnamed senior interrogator described an unidentified black site as "good for interrogations" because it was "the closest thing he has seen to a dungeon, facilitating the displacement of detainee explanations."
Spectators heard the audio on a 40-second delay from the gallery at the back of court, separated by triple-pane glass. "It's hard to imagine a more rich and vivid description than those statements," Mr. Groharing said.
Defense lawyers called the written accounts sanitized versions of the eyewitness testimony they sought.
Mr. Mohammed's lawyer, David Nevin, said the term rectal rehydration "is a polite way of saying rape with the insertion a foreign object into the rectum. But how is it done? I'd like to know, how is it done?"
One small detail can change a juror's mind about whether to vote for capital punishment, Mr. Nevin has said.
Eugene R. Fidell, who teaches military law at Yale Law School, said a showdown over black site evidence was foreseeable.
"The defense lawyers have to have the tools with which to perform their duty, especially in capital cases. No question," Mr. Fidell said. "Somebody should have thought about that before they started torturing these people."
He added: "This was an accident waiting to happen. The only thing that surprises me is this is 2019 and the problem remains unresolved."