A military judge ruled on Wednesday that plea agreements in the Sept. 11 case were valid, reviving the possibility that the man accused of planning the attacks, Khalid Shaikh Mohammed, and two accused accomplices could eventually be sentenced to life in prison instead of death.
Col. Matthew N. McCall, the judge, ruled that Defense Secretary Lloyd J. Austin III acted too late and beyond the scope of his authority when he rescinded the three separate pretrial agreements on Aug. 2, two days after a senior Pentagon appointee signed them.
The decision was the latest to inject uncertainty into the long-running case at Guantánamo Bay against Mr. Mohammed and four others who were charged in 2012 with conspiring in the attacks that killed nearly 3,000 people on Sept. 11, 2001.
Prosecutors disclosed the deal with three of the defendants this summer. They said it was meant to bring some “finality and justice” to the case, which had been mired in litigation over the C.I.A.’s torture of the defendants and other issues.
Prosecutors and the office of the secretary of defense had no immediate comment on whether the government would appeal. Rear Adm. Aaron C. Rugh, the chief prosecutor for military commissions, said his team was “discussing next steps.”
“We are reviewing the decision and don’t have anything further at this time,” said Maj. Gen. Patrick Ryder, the Pentagon’s press secretary.
The senior official overseeing military commissions, Susan K. Escallier, a retired Army lawyer whom Mr. Austin had appointed to the job, signed the agreement that had been negotiated by prosecutors across more than two years on July 31. Mr. Austin was traveling abroad and aides said he was surprised by the development.
On Aug. 2, Mr. Austin declared that the case was of such significance that a full trial should be held and rescinded the deal. He stripped Ms. Escallier of the authority to reach the deal.
But Colonel McCall said Ms. Escallier “possessed the legal authority” to sign the agreements when she did. He called them “enforceable contracts with the classic elements of offer, acceptance and consideration.”
Before Ms. Escallier acted, the judge said, Mr. Austin had the power to retain the role of overseer of the case himself, something he had never done. “What the secretary of defense could not do, however, was delegate authority to Ms. Escallier, recognize her independent discretion, then reverse that discretion upon disagreeing with how that discretion was utilized.”
Colonel McCall said he would move forward with having Mr. Mohammed and two other defendants, Walid bin Attash and Mustafa al-Hawsawi, appear before his court to enter their pleas, separately. But he set no timetable, perhaps to give prosecutors time to decide whether to appeal.
The deals themselves are under seal. In a footnote, Colonel McCall wrote that two of the defendants, Mr. Mohammed and Mr. Hawsawi, had clauses in their agreement in the event the government withdrew from it: The case could go forward, but not as a death penalty trial.
So, he said, if a higher court overruled him, sided with Mr. Austin and again canceled the plea agreement, a court would then have to decide whether the breach of contract clause was valid — and Mr. Mohammed and the others would face a maximum of life in prison at their trial.
He issued the decision hours after arriving at Guantánamo Bay on the eve of the resumption of pretrial hearings in the case for another defendant, Ammar al-Baluchi, who did not reach a plea deal. The fifth defendant, Ramzi bin al-Shibh, has been found incompetent to stand trial or reach a plea agreement.
A forensic psychiatrist is expected to testify on Thursday on the overarching question of whether confessions the defendants made in 2007, after years in secret C.I.A. prisons, were voluntary or the product of torture.
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