Defense Secretary Lloyd J. Austin III on Friday overruled 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 a memorandum relieving the senior Defense Department official 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. He left Ms. Escallier in the role of oversight of Guantánamo’s other cases.

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.”

Mr. Austin’s decision brought relief to family members of victims who had expressed anger over the deal, but it also left uncertain the next steps of the prosecution over America’s deadliest terrorist attack.

Before this week’s developments, jury selection in the 12- to 18-month trial was not envisioned to start before 2026, meaning a verdict was likely to be years away. The case had become mired in more than a decade of pretrial proceedings that focused on whether the detainees’ torture in secret C.I.A. prisons had contaminated the evidence against them.

With the plea deal upended, the military judge, Col. Matthew N. McCall, is likely to resume hearing testimony next week. He had been working toward deciding a series of challenges brought by defense lawyers, including whether to exclude confessions that were key to the government’s case.

Ms. Escallier’s approval of the plea agreement, which was reached between prosecutors and the defendants over two years of negotiations, had appeared to resolve the long-running case of the men, who have been in U.S. custody since 2003. The military judge was preparing to question Mr. Mohammed, possibly as soon as Wednesday, about whether he understood and voluntarily agreed with the plea.

Mr. Austin was traveling abroad at the time the deal was approved and returned to the United States later that day.

By then, prosecutors in the case had told family members of those killed in the attacks about the agreement, and some reacted with disappointment and anger that a death sentence was no longer possible. On Friday, those families expressed appreciation for Mr. Austin’s intervention.

“This is a really welcome development,” said Terry Strada, whose husband, Tom Strada, a bond broker, was killed at the World Trade Center. “I’m happy to see the Pentagon getting involved. And glad the death penalty is back on the table. Otherwise, how could we be assured some administration would not commute their sentence or swap them in the future?”

“Thank god,” said Kathleen Vigiano, a former police officer whose New York police detective husband, Joseph, and firefighter brother-in-law, John, were both killed at the World Trade Center. She said she had long been eager for a Sept. 11 trial to answer questions about “how this was planned, and who knew what.”

e called the announcement a gift for the family, which was celebrating the 84th birthday of her husband and brother-in-law’s mother, Jeanette Vigiano. “It was a great birthday present for her,” she said.

Mr. Austin’s action was met with disbelief by lawyers at Guantánamo Bay, who had negotiated the plea deal across 27 months, even as they were preparing for an eventual trial.

“I am respectfully and profoundly disappointed that after all of these years the government still has not learned the lessons of this case, and the mischief that results from disregarding due process and fair play,” said Gary D. Sowards, Mr. Mohammed’s lead lawyer.

A senior Pentagon official said that the decision was the secretary’s alone, and that the White House had no involvement. The official said Mr. Austin had never supported a plea deal and wanted the military commission trials to proceed.

Republican leaders had been pushing to overturn the deal.

Senator Mitch McConnell of Kentucky, the longtime Republican leader, called the agreement “a revolting abdication of the government’s responsibility to defend America and provide justice.”