A panel of federal appeals court judges on Friday threw out a plea agreement in a 2-1 decision that would have allowed 9/11 mastermind Khalid Sheikh Mohammed and other co-defendants to plead guilty in exchange for escaping the federal death penalty.

The deal, negotiated over two years, would have given Mohammed and the co-defendants life without parole.

The military prosecution of Mohammed and other defendants has been ongoing for more than two decades, snarled by preliminary hearings and challenges over evidence lawyers for the defense said had been obtained by torture.

The Biden administration's Defense Department announced in July that it entered pretrial agreements with Mohammed and three co-conspirators of the 9/11 attack. But then-Defense Secretary Lloyd Austin overrode the agreement just two days later, reserving himself at the sole authority to enter into such agreements.

A military appeals court that December ruled against Austin's efforts, putting the agreement to avoid the death penalty back in place.

On Friday, the U.S. Court of Appeals D.C. Circuit tossed the plea agreement, determining that Austin acted within his authority.

"In light of the clear and indisputable errors committed by the military judge, which implicate issues of immense national importance, we conclude that issuance of the writs is appropriate under these circumstances," Appeals Judges Patricia Millett and Neomi Rao, wrote.

Judge Robert Wilkins, however, sharply dissented from the majority’s decision, calling the move to overturn a military judge “stunning.”

“Our deference should be at its zenith when military courts follow persuasive military precedent in the construction of military rules. I am befuddled,” he wrote.

Mohammad is accused to being the mastermind of the deadliest attack on U.S. soil when hijacked planes flew into the World Trade Center in New York and the Pentagon. A fourth hijacked plane crashed in Pennsylvania.

Updated 2:10 p.m.

Zach Schonfeld contributed.