For years, a thorny question has dominated pretrial hearings in the military commissions case over the Sept. 11, 2001, attacks: Did the men accused of plotting them voluntarily confess in 2007 after the C.I.A. had stopped torturing them, and could those statements be used as evidence at their eventual death-penalty trial?
So it came as a surprise when a veteran F.B.I. analyst revealed that in 2009, when the Obama administration was planning to instead try the men in civilian court, federal prosecutors had decided against trying to offer the statements as evidence.
The revelation sets in stark relief the contrary decision by military prosecutors to build their case around summoning the F.B.I. interrogators as witnesses, calling such potential testimony their “most critical” evidence. It also underlines how that decision has opened the door to years of litigation and contributed to a lengthy delay in getting the case to trial.
Brig. Gen. Mark S. Martins, the chief prosecutor at Guantánamo from 2011 until his retirement in 2021, did not respond to a request for comment.
During a closed hearing on March 6, Kimberly Waltz, a supervisory intelligence analyst at the F.B.I. who works on the Guantánamo prosecution team, disclosed that civilian prosecutors had decided the statements were unnecessary. In 2009, when she helped the civilian prosecution team evaluate the evidence, federal prosecutors rejected using the confessions at trial, according to a transcript of the hearing recently released by the government.
“At that time it was my understanding,” she said, that “we were not going to be able to use them; they weren’t admissible.”
In an interview, Adam S. Hickey, a former federal prosecutor who was part of the 2009 civilian team, confirmed that the team had decided, for “strategic reasons,” against trying to use the statements in federal court. The confessions were not necessary to prove the men’s guilt, the prosecutors believed, and it was not worth arguing over whether they were made voluntarily.
“We did not spend much time analyzing the legal question,” he said. The thinking was, “Let’s just have a clean break.”
Ms. Waltz gave a simpler reason. Before the prisoners spoke to the federal agents, “They were not Mirandized.”
The Miranda warning is the notice that police read to inform people in custody that anything they say can and will be used against them in court and that they have the right to remain silent and to have a lawyer present during questioning. The Supreme Court required it to protect the Fifth Amendment right against self-incrimination. Prosecutors can use statements that people made in custody as courtroom evidence if the defendants had received the warning.
But it is not clear whether or how the Fifth Amendment applies to noncitizens held at Guantánamo. Under a 2009 law, military commissions standards are more flexible, allowing such statements if a judge decides they were “voluntarily given” and reliable.
The bid by military prosecutors to use the confessions has set off a prolonged fight as lawyers explore the years of torture and solitary confinement the defendants underwent before the F.B.I. talked to them.
The four Guantánamo prisoners who are accused of conspiring in the Sept. 11 plot were captured in 2003. They were held by the C.I.A. in “black site” prisons and tortured. A fifth such detainee, Ramzi bin al-Shibh, was originally part of the case, too, but has been declared mentally unfit to stand trial — a condition his lawyer blames on his torture.
In 2006, the Bush administration had the men moved to Guantánamo for trial, and they were questioned anew by so-called F.B.I. clean teams uninvolved with the torture. Defense lawyers, arguing to suppress those statements, say that they were tainted by what happened before.
For example, the C.I.A. had forced Khalid Shaikh Mohammed, who is accused of being the architect of the hijackings, to talk to interrogators through waterboarding, rectal abuse, shackling while nude and other brutality. He had been in U.S. custody for more than 1,400 days by the time federal agents questioned him and his co-defendants in 2007.
The idea was to use those interrogations as confessions in a military trial at Guantánamo Bay. But in 2009, Attorney General Eric H. Holder Jr. decided instead to hold the trial in a civilian court in New York, and prosecutors obtained a grand jury indictment of the men that year.
The plan met steep political resistance, and Congress blocked it. Military prosecutors charged the current case at Guantánamo in 2012.
It has since come to light that there is another source of incriminating statements by the defendants: The government had secretly bugged a prison yard at Guantánamo and had recordings of them talking to other prisoners about the plot.
For example, the government has disclosed a translation of an overheard Arabic conversation in the prison yard in 2009, in which another defendant, Ammar al-Baluchi supposedly said to a fellow detainee: “Three-quarters of the money for the operation was sent through me.”
Those recordings and other available evidence apparently persuaded the civilian prosecutors that they had enough to win convictions without confessions. Additional evidence being offered for the Guantánamo trial includes bank records, videos and intercepted telephone calls.
Military prosecutors, however, have devoted years to defending the disputed evidence that the federal prosecutors planned to forgo. They want a “Law & Order” moment with Frank Pellegrino, a retired F.B.I. agent who tracked Mr. Mohammed for years, describing for a military jury how he and Mr. Mohammed spent four days in January 2007 discussing the Sept. 11 plot.
At the direction of Bush administration lawyers, who believed the Supreme Court’s 1966 ruling in Miranda v. Arizona did not apply at Guantánamo — a notion that defense lawyers contest — Mr. Pellegrino and other F.B.I. agents did not start with the warning from that case.
They read from a different script that merely told prisoners that talking was optional and that they would not be returned to the people who held them before. When Mr. Mohammed asked for a lawyer, the request was brushed aside.
The decision to try to use the confessions has complicated the case for years.
In 2018, the first military judge in the case, Col. James L. Pohl, threw out the confessions, citing limits on defense lawyers’ ability to investigate the C.I.A. years, then retired. But the next judge reinstated them to determine whether defense lawyers could mount a meaningful challenge.
Since 2019, the court has heard 140 hours of wide-ranging testimony about both the C.I.A. program and the defendants’ years of solitary confinement at Guantánamo Bay as it explores whether the 2007 statements were voluntary.
The efforts by defense lawyers have surfaced new details from the black sites that in turn have helped the lawyers spin up motions to dismiss the case or take the death penalty off the table. Among their arguments: The detainees were not informed of their Miranda rights, the government’s conduct was outrageous and the prisoners were subjected to unlawful punishment even before their trial.
The same issue arose in Guantánamo’s other capital case, against a detainee who is accused of conspiring in the 2000 bombing of the U.S.S. Cole. Last year, a judge suppressed that defendant’s 2007 statements to the F.B.I., writing that his will to resist incriminating himself had been “intentionally and literally beaten out of him” in C.I.A. custody. Prosecutors are appealing.
In the Sept. 11 case, Mr. Pellegrino and Ms. Waltz have both testified that they saw voluntary law enforcement interviews that were separate and apart from the C.I.A. era, a time that Mr. Pellegrino described as a “flaming bag of crap that we got stuck with.”
But last week, Dr. Charles A. Morgan III, a former psychiatrist at the C.I.A., testified that its abuse had embedded such fear in Mr. Baluchi’s psyche that he could not distinguish between the F.B.I.’s interrogations and earlier ones by the C.I.A. The C.I.A. program, he said, rendered “people malleable in order to have them act in ways that were not in their own interests.”
The current judge, Col. Matthew N. McCall, has said that he hoped to resolve the admissibility question before he retires at the end of the year. Last week, he said, he would consider extending his time on the bench into 2025.
In an interview, Mr. Holder said that had his plan to try the men in the United States happened, the case would be long over.
“The politicians and hacks who second-guessed my decision to bring cases in the effective federal courts should be ashamed,” he said. “Had it not been for their political machinations, Khalid Shaikh Mohammed would just be a bad memory now.”