A military judge has yet to decide whether Defense Secretary Lloyd B. Austin III successfully canceled a plea agreement in the Sept. 11 terrorism case. Butagilaplay, even if Mr. Austin did, a clause in the deal may mean the government can no longer seek the death penalty in a trial of Khalid Shaikh Mohammed, accused of being the mastermind of the attacks.

Mr. Mohammed’s 20-page plea agreement is under seal at the court. But five people with knowledge of its contents described the breach of contract clause on the condition they not be identified because of the sealing order. It says if the government withdraws from the deal and the defendants have not violated their side of it, any future trial takes the death penalty off the table.

One called the bailout clause “a poison pill.”

The disclosure is the latest development to inject uncertainty into the future of the long-running military case at Guantánamo Bay that accuses Mr. Mohammed and four other prisoners there of helping to orchestrate the hijackings that killed nearly 3,000 people on Sept. 11, 2001.

The case had appeared to be partially settled on July 31, when the Defense Department announced in a two-paragraph statement that a senior Pentagon official, Susan K. Escallier, had reached plea deals with Mr. Mohammed and two other defendants in the case in her role as overseer of the war court. They would plead guilty to their roles in the attacks in exchange for life sentences rather than face a death-penalty trial.

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Two days later, Mr. Austin stripped Ms. Escallier, his appointee, of the authority to reach a deal, citing “the significance of the decision to enter into pretrial agreements.” In the same brief memo, he announced that he was withdrawing from the agreements.

He later elaborated that he believed the case should go to trial but made no mention of whether it needed to be a capital punishment case.

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