In late 2006, in an effort to turn the page on a legacy of state-sponsored torture, prosecutors for the George W. Bush administration began an experiment at Guantánamo Bay. They set up teams of law enforcement officers to try to obtain voluntary confessions from men who had spent years in brutal conditions in isolated C.I.A. prisons.
A military judge declared that experiment a failure, at least in one case.
In a wide-ranging ruling, Col. Lanny J. Acosta Jr. threw out a confession that federal agents at Guantánamo Bay obtained in 2007 from a Saudi prisoner who is accused of plotting the suicide bombing of the U.S.S. Cole on Oct. 12, 2000. The attack, in the port of Aden, Yemen, killed 17 U.S. sailors.
The agents testified that they were courteous and friendly to the prisoner, Abd al-Rahim al-Nashiri, and made clear to him that his participation in interrogations in January and February of 2007 was voluntary.
But Mr. Nashiri, who was arrested in 2002, had spent four years in secret C.I.A. prisons, where interrogators used violence, threats and punishment to get him to talk. The judge wrote on Aug. 18 that “any resistance the accused might have been inclined to put up when asked to incriminate himself was intentionally and literally beaten out of him years before.”
In other words, Colonel Acosta found that the “clean team” interrogations at Guantánamo, as they were called, could not undo the damage of C.I.A. torture and years of conditioning to compel prisoners to answer questions on demand.
The 50-page ruling is the first major decision, based on evidence presented in pretrial hearings, about the admissibility of interrogations by federal agents who were supposed to build fresh cases against men who had spent years in secret C.I.A. prisons known as black sites.
Although the ruling does not set a precedent and prosecutors are already appealing it, the decision has shaken a foundation on which prosecutors built their cases against men accused of plotting Al Qaeda attacks.
Its impact has yet to be seen on the court’s better-known case accusing five prisoners of conspiring in the Sept. 11, 2001, attacks. Both are death penalty cases, and defense lawyers in the Sept. 11 case are similarly calling witnesses to argue that confessions were tainted by C.I.A. torture. But another military judge is presiding in that matter and is not bound by the Cole decision.
But Jeffrey D. Groharing, a veteran prosecutor in Sept. 11 pretrial proceedings, has called the defendants’ confessions at Guantánamo Bay “the most critical evidence in this case.”
Next month, prosecutors in that case plan to call on the testimony of Frank Pellegrino, a retired F.B.I. agent. As a member of a “clean team” in 2007, he listened as Khalid Shaikh Mohammed, the man accused of being the mastermind of the Sept. 11 attacks, described his role. The government argues that Mr. Mohammed voluntarily incriminated himself in his fourth month at Guantánamo Bay, nearly four years after he was taken into U.S. custody.
By then, C.I.A. interrogators had waterboarded Mr. Mohammed 183 times. He had also been kept in chains, left nude, deprived of sleep and isolated — many of the same techniques that were first used on Mr. Nashiri. Both men were threatened with return to “the hard times” if they did not cooperate with their captors in the black sites under the rendition, detention and interrogation program.
Colonel Acosta’s ruling “drives home that it is actually not possible to sanitize cases against people who were in the R.D.I. program,” said Stephen I. Vladeck, a professor at the University of Texas School of Law who has studied the war court. “It is not as if this decision conclusively settles this question for every case. But both in its reasoning and in its symbolism I think it’s going to be a de facto precedent.”
Many of the issues are the same. Like Mr. Nashiri, two of the men accused of conspiring with Mr. Mohammed in the Sept. 11 attacks were held incommunicado by the C.I.A. at Camp Echo in Guantánamo in 2003 and 2004 — the same prison compound where federal agents got defendants to confess in 2007.
U.S. military doctors have diagnosed Mr. Nashiri with post-traumatic stress disorder, for which, Colonel Acosta noted, he has apparently never been treated. Next month, the judge in the Sept. 11 case is expected to hear from medical experts on why they recently found one of the accused Sept. 11 plotters, Ramzi bin al-Shibh, not competent enough to be tried or plead guilty.
In his decision suppressing Mr. Nashiri’s confession, the judge cited the forensic psychiatrist Michael Welner, who had testified as a government expert.
Dr. Welner had argued that, based on his interpretation of prison documents and transcripts, Mr. Nashiri freely chose to confess. But the judge rejected that opinion, citing testimony from Dr. Welner in which he had also said that if someone had a choice between compliance and “extreme pain or suffering, then that’s not a real choice.”
Dr. Welner is also a government paid expert on the issue of Mr. bin al-Shibh’s sanity.
“Since the early 20th century, medical knowledge has concluded that there is no medical reason to conduct so-called ‘rectal feeding,’” Colonel Acosta wrote. “Although fluids can be absorbed through the rectum in emergencies, food or nutrition cannot.”
The case is not over. The judge has approved other evidence prosecutors want to use at his trial, including hearsay testimony, to be delivered by federal agents, that people in Yemen saw Mr. Nashiri near the port of Aden two months before bombers blew up the Cole.
Colonel Acosta also allowed prosecutors to present what Mr. Nashiri told a military panel at Guantánamo later in 2007. At a status hearing, he admitted to knowing Osama bin Laden and receiving money from him for an unrealized shipping business project in the Persian Gulf, but he denied being a member of Al Qaeda and recanted earlier confessions, which he said were to stop his torture.
Yet to be seen is whether prosecutors, as they have in the Sept. 11 case, propose that Mr. Nashiri plead guilty to certain crimes in exchange for a life sentence, rather than the possibility of execution.
Colonel Acosta retires from the Army next month after 25 years of service. A new judge, Lt. Col. Terrance J. Reese of the Marines, was appointed to navigate the 12-year-old case to trial.