A military judge on Sunday postponed a hearing to receive the guilty plea of Khalid Shaikh Mohammed, who is accused of masterminding the Sept. 11 attacks, so that prosecutors can seek again to nullify the plea deal.
Col. Matthew N. McCall, the judge, did not freeze preparations for the hearing, as prosecutors had requested. Instead, he told defense and prosecution lawyers to agree on a week or more next month or in early January to hold plea hearings at Guantánamo Bay, Cuba, for Mr. Mohammed and his co-defendants, Walid bin Attash and Mustafa al-Hawsawi.
The judge said it was “not reasonable to indefinitely delay” the entry of pleas in the case. He also told the sides to continue to collaborate on providing answers to questions related to clauses in the plea agreements. All three plea deals were reached July 31 and ostensibly withdrawn by Defense Secretary Lloyd J. Austin III two days later. On Wednesday, however, the judge ruled that Mr. Austin had acted too late and that the pleas were still valid, lawful contracts.
Colonel McCall made no mention of the fact that his next scheduled hearing, from Jan. 20 to Jan. 31, straddled the inauguration of President-elect Donald J. Trump — and most likely Mr. Austin’s departure from the Pentagon.
But a defense lawyer noted that the official who had approved the deal — an Austin appointee — was likely to leave the Pentagon at the end of the Biden administration and could potentially become unavailable for questions related to aspects of the plea deals.
In a rare Sunday hearing, Clayton G. Trivett Jr., the lead prosecutor, told the judge that the chief prosecutor for military commissions, Rear Adm. Aaron C. Rugh, had instructed his staff on Friday night to prepare an appeal of the judge’s decision reinstating the guilty pleas. Mr. Trivett asked the judge to halt all plea-related proceedings.
Defense lawyers opposed the request. Gary D. Sowards, Mr. Mohammed’s lawyer, said the impact of the decision to appeal was that “the promise of finality and justice in the case has been snatched away” again.
Mr. Sowards mentioned people at the rear of the court who were watching the proceedings, representing victims of the terrorist attacks that killed nearly 3,000 people on Sept. 11, 2001. Some of them had traveled to Guantánamo Bay to see Mr. Mohammed plead guilty.
Relatives of the victims have described the experience of the plea deals being reached and then undone as an emotional roller coaster.
There has never been a unified view among the thousands of family members on how the case should be resolved. Some want what prosecutors have called judicial finality, or a guilty plea in exchange for life sentences without the possibility of appeal or release. Others insist on an eventual capital trial, although a clause in Mr. Mohammed’s plea agreement may require that if there is a trial, it should go forward with the death penalty off the table.
Under the statute that created the war court, the prosecutors were not automatically entitled to appeal the judge’s ruling last week that the plea deals were valid. Instead, prosecutors said they would ask the U.S. Court of Military Commission Review to take the extraordinary step of issuing a writ of mandamus on the question.
To get the higher court panel to look at Judge McCall’s decision, the prosecutors must persuade the panel that they have a likelihood of successfully arguing that Judge McCall was wrong in reinstating the plea agreements — and that Mr. Austin had the authority to retroactively cancel them.
But the special court, which is made up of military and civilian judges, does not convene regularly and has at times taken months or years to decide cases.
Mr. Trivett and other prosecutors on the Sept. 11 case negotiated all three of the plea deals over two years. Susan K. Escallier, a retired general and former career Army lawyer, approved the deals. Mr. Austin put her in charge of military commissions last year.
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