Defense Secretary Lloyd J. Austin III on Friday relieved the overseer of the war court at Guantánamo Bay and revoked a plea agreement reached earlier this week with the accused mastermind of the Sept. 11, 2001, attacks and two alleged accomplices.

The Pentagon announced the decision with the release of a memorandum relieving the senior official at the Defense Department responsible for military commissions of her oversight of the capital case against Khalid Shaikh Mohammed and his alleged accomplices for the attacks that killed nearly 3,000 people in New York City, at the Pentagon and in a Pennsylvania field.

The overseer, retired Brig. Gen. Susan K. Escallier, signed a pretrial agreement on Wednesday with Mr. Mohammed, Walid bin Attash and Mustafa al-Hawsawi that exchanged guilty pleas for sentences of at most life in prison. In taking away the authority, Mr. Austin assumed direct oversight of the case and canceled the agreement, effectively reinstating it as a death-penalty case.

Because of the stakes involved, the “responsibility for such a decision should rest with me,” Mr. Austin said in an order released Friday night by the Pentagon.

“Effective immediately, in the exercise of my authority, I hereby withdraw from the three pretrial agreements that you signed on July 31, 2024.”

Ms. Escallier’s approval of the agreement that was reached between prosecutors and the defendants over two years of negotiations had appeared to resolve the case, which had been mired in pretrial hearings since 2012. Some family members of those killed in the attacks reacted with anger that a death sentence was no longer possible.

Mr. Austin was traveling abroad and returned to the United States later that day.