How the 9/11 Plea Deal Came Undone

In the space of three days last week, the Sept. 11 case was rocked by two decisions that stunned victims’ families and jolted a political debate.

First, a Pentagon official authorized a plea agreement meant to resolve the case with lifetime sentences. Then, Defense Secretary Lloyd J. Austin III abruptly canceled the deal, reviving the possibility that the man accused of planning the attacks, Khalid Shaikh Mohammed, and two accused accomplices could someday face a death penalty trial.

Suddenly, a case that had mostly drifted from public consciousness in 12 years of pretrial proceedings was back in the spotlight and no closer to the trial that some relatives of the nearly 3,000 victims had been aching for at Guantánamo Bay.

This account of those fateful three days is based on interviews and conversations with Pentagon officials, Sept. 11 family members and parties to the case.

There was no hint of what would come on this day in the mostly forgotten case at Guantánamo Bay.

The court was in a closed hearing — no public, no defendants — as a retired Army officer testified about his time in charge of the secret prison where the defendants were held, beginning in 2006. It was the 51st round of pretrial hearings.

But at some point, in an office near the Pentagon, a senior Defense Department official who is responsible for military commissions approved a plea agreement with Mr. Mohammed and the two accused of being accomplices.