The man accused of being the mastermind of the Sept. 11 attacks, Khalid Shaikh Mohammed, has agreed to let government prosecutors use portions of a 2007 confession that he says were obtained through his torture at any future sentencing trial if his case is settled with a life sentence.
Defense lawyers have been trying for years to have those confessions excluded from the death-penalty trial against Mr. Mohammed and three other men accused of plotting the Sept. 11, 2001. The lawyers had argued that he was conditioned to answer his captors’ questions in a secret C.I.A. prison network where he was waterboarded, beaten and subjected to rectal abuse.
But an excerpt from his plea deal that was released by a federal court over the weekend shows that Mr. Mohammed agreed that prosecutors can use certain portions of his disputed confessions against him at a sentencing trial — if he is allowed to plead guilty.
That deal is in the midst of a heated political and legal controversy that is spilling over into the Trump administration.
On July 31, after more than a decade of litigation, a senior Pentagon appointee signed separate agreements with Mr. Mohammed, Walid bin Attash and Mustafa al-Hawsawi to settle their capital case in exchange for their giving up the right to appeal their convictions and challenge certain evidence. Those deals were submitted to a military judge, under seal.
Then, two days later, Defense Secretary Lloyd J. Austin III moved to withdraw from the deals. He retroactively stripped his appointee, Susan K. Escallier, a retired Army lawyer, of the authority to reach the deal and said he wanted the men to face trial.
Now a federal court has halted their entry of pleas while it decides whether Mr. Austin had the authority to breach the contract and whether to return the case to a full trial.
The court’s release of a few of the excerpts from the plea agreement comes at a pivotal time.
Hearings are still underway at Guantánamo Bay in the case of Ammar al-Baluchi, the fourth defendant in the case. The military judge, Col. Matthew N. McCall, is set to decide whether to exclude Mr. Baluchi’s confessions from his death-penalty trial, as they were obtained through torture.
Mr. Baluchi’s case has proceeded without the participation of legal teams for the three men who have sought to plead guilty to avert eventual death-penalty trials.
There is a precedent for a military commission suppressing the confessions. In August 2023, an Army judge threw out the same type of evidence in Guantánamo’s other capital case, against a prisoner who is accused plotting the bombing of the U.S.S. Cole in 2000. Prosecutors are appealing to get his 2007 interrogations by the F.B.I. reinstated.
In Washington, the Court of Appeals for the District of Columbia Circuit has scheduled arguments for Jan. 28 on whether the other three defendants’ plea deals can go forward. The case was brought on Mr. Austin’s behalf by Biden administration appointees at the Justice Department who will leave the job on Monday.
Career Justice Department lawyers have now taken over the case and submitted the excerpts, by agreement with the military commissions defense lawyers of Mr. Mohammed, Mr. bin Attash and Mr. Hawsawi. The court filing also revealed that Mr. Bin Attash and Mr. Hawsawi have likewise agreed to have portions of their 2007 confessions used against them at their sentencing trial, if the pleas go forward.
But the Trump administration has not signaled how it will deal with the plea agreements. Colonel McCall, the judge, has said that if the circuit court resolves the case in favor of the pleas, he could hold proceedings in February. If the deal falls apart, the defense lawyers would go back to trying to keep the confessions out of the trial.
Like his co-defendants, Mr. Baluchi spent more than three years in C.I.A. custody after his capture in Pakistan in 2003 and was moved to Guantánamo Bay in September 2006. Within months of his transfer there, F.B.I. agents were brought in to interrogate the men for evidence to be used at their trial.
His lawyers have argued that in those early months, he had no reason to believe he could provide his interrogators with answers other than those he gave to the C.I.A. for years.
Lawyers for all four men also have also asked the judge to discard transcripts of their appearances in early 2007 before a panel of military officers called combatant status review tribunals. They argue that those, too, are tainted by torture.
At Mr. Mohammed’s March 10, 2007, tribunal, an unidentified U.S. military officer read aloud a statement he said was submitted by Mr. Mohammed: “I was responsible for the 9/11 operation, from A to Z.”
Excerpts from the plea agreement show that Mr. Mohammed also agreed to have portions of that transcript used against him at his sentencing trial.
Clayton G. Trivett Jr., the lead prosecutor who negotiated the plea deal, has described plans for a sentencing trial that he said would start late this year and most likely extend into 2026.
The sentencing would include a monthslong presentation to the panel and the public “to establish a historical record of the accuseds’ involvement in what happened on Sept. 11,” he said, as well as potentially hundreds of victim impact statements from survivors or relatives of those killed.
