A federal appeals court on Friday overturned a plea deal to resolve the Sept. 11, 2001, case with life sentences, a decision that could restart proceedings toward a lengthy death penalty trial at Guantánamo Bay.

The 2-to-1 decision was the latest upheaval for families awaiting a resolution in the long, agonizing case and does not mean the conspiracy trial can start soon. More appeals could come. Also, the previous military judge retired recently, and his replacement will need to read the voluminous record and decide threshold issues, including whether confessions prosecutors want to use were unlawfully obtained through torture.

A senior Pentagon official reached the deal in the summer of 2024 with Khalid Shaikh Mohammed, the man accused of being the mastermind of the plot, and two other defendants. Under the agreement, each would admit to his role in the plot to avert a capital trial.

Image A portrait of Khalid Shaikh Mohammed at Guantánamo Bay in 2022, provided by his attorneys.

Within days of the deal, Defense Secretary Lloyd J. Austin III declared it void. But the judge in the case found that he was bound to the contract reached by the senior Pentagon official in charge of the war court, a retired Army lawyer whom Mr. Austin had appointed.