GUANTÁNAMO BAY, Cuba >> The man accused of plotting the attacks of Sept. 11 and two of his accomplices have agreed to plead guilty to conspiracy charges in exchange for a life sentence rather than a death-penalty trial at Guantánamo Bay, Cuba, prosecutors said today.

A senior Pentagon official approved the deal for Khalid Sheikh Mohammed, Walid bin Attash and Mustafa al-Hawsawi, according to Defense Department officials with knowledge of the agreement. The men have been in U.S. custody since 2003. But the case had become mired in more than a decade of pretrial proceedings that focused on the question of whether their torture in secret CIA prisons had contaminated the evidence against them.

Word of the deal emerged in a letter from war court prosecutors to family members of victims of the attacks on Sept. 11, 2001.

“In exchange for the removal of the death penalty as a possible punishment, these three accused have agreed to plead guilty to all of the charged offenses, including the murder of the 2,976 people listed in the charge sheet,” said the letter, which was signed by Rear Adm. Aaron C. Rugh, the chief prosecutor for military commissions and three lawyers on his team.

The letter said the men could submit their pleas in open court as early as next week.

The plea averted what was envisioned as an eventual 12- to 18-month trial, or, alternatively, the possibility of the military judge throwing out confessions that were key to the government’s case. Col. Matthew N. McCall, the judge, had been hearing testimony this week and had more hearings scheduled for later this year to decide that and other key pretrial issues.

Mohammed, a U.S.-educated engineer and avowed jihadist, was accused of coming up with the idea of hijacking airplanes and flying them into buildings. Prosecutors said he presented Osama bin Laden with the idea in 1996, and then helped train and direct some of the hijackers.

He and Hawsawi were captured together in Pakistan in March 2003, and held in secret CIA prisons until their transfer to the U.S. naval base at Guantánamo in September 2006 for an eventual trial. By then, agency interrogators had held them for years incommunicado and tortured them, including subjecting Mohammed to a record 183 rounds of waterboarding, a decision that would stymie years of efforts to put the men on trial.

The three men will still face a mini trial of sorts, but probably not before next year. At the military commissions, where they were charged, a judge accepts the plea, but a military jury must be empaneled to hear evidence, including testimony from victims of the attacks, and deliver a sentence. Before that, the military judge has typically resolved litigation over what evidence can be used at the sentencing proceeding.

Two of the original five defendants were not a party to the deal. Ramzi Binalshibh, who was accused of helping to organize a cell of the hijackers in Hamburg, Germany, was found incompetent to stand trial because of mental illness, and his case was severed.

The fifth defendant, known as Ammar al-Baluchi, was not a party to the plea agreement and could face trial alone. He is the nephew of Mohammed and is charged, like Hawsawi, with helping the hijackers with finances and travel arrangements while working in the Persian Gulf.

Plea deals had been under discussion since March 2022 but hit a significant snag in September when the White House declined to sign off on conditions sought by the defendants.

The men wanted assurances that they would not serve their sentences in solitary confinement, would have improved contact with their families and continued contact with their lawyers. Baluchi in particular also wanted the United States to pledge to set up a special torture treatment program for them at the prison.

The Biden administration considered the request for more than a year and then declined to weigh in. It was not known if any of the conditions were contained in the agreement reached by Susan Escallier, the senior Pentagon official responsible for overseeing the war court.

The development came in the midst of the 51st round of pretrial hearings in the case since arraignment in 2012. Mohammed and the others were last seen in court almost two weeks ago, for testimony from a psychologist who had interrogated him and other CIA prisoners.

Prosecutors were under conflicting pressures over what to do with the case. Some family members were fearful that it would never reach a resolution, and that the defendants would die in U.S. custody without a conviction. Others, wanting a death penalty, pressed the government to get the case to trial, even at the risk of the sentence being later overturned.

Rugh and his colleagues wrote in their letter to the families that their decision to agree to guilty pleas after “12 years of pretrial litigation was not reached lightly. However, it is our collective, reasoned and good-faith judgment that this resolution is the best path to finality and justice in this case.”

It was also signed by Clayton G. Trivett Jr. and Jeffrey D. Groharing, two military prosecutors who had been on the case since the start.

This article originally appeared in The New York Times.

© 2024 The New York Times Company