WASHINGTON – The Department of Defense will appeal a the decision of the military judge that the plea deals struck by Khalid Sheikh Mohammed, the alleged mastermind of the Sept. 11, 2001 attacks, and two of his co-defendants are valid, a defense official said Saturday.

Last week’s ruling overruled Defense Secretary Lloyd Austin to drop the bids and concluded that the plea agreements were valid. The judge granted the three pleas and said he would schedule them for a future date to be determined by the military commission.

The department will also request that any hearing on the reasons be postponed, according to the official, who was not authorized to publicly discuss legal matters and spoke on condition of anonymity. ContraaDM. Aaron Rugh, the chief prosecutor, sent a letter to the families of the 9/11 victims on Friday informing them of the decision.

The judge’s ruling, Air Force Col. Matthew McCall, allowed the three 9/11 defendants to enter guilty pleas in the U.S. military courtroom in Guantanamo Bay, Cuba, and would spare them the risk of the death penalty. The pleas by Mohammed, Walid bin Attash and Mustafa al-Hawsawi would be a key step toward closing the government’s long-running and legally troubled trial into the attacks that killed nearly 3,000 people.

Government prosecutors had negotiated the plea deals with defense lawyers under government auspices, and the top Guantanamo military commission official approved the deals. But the deals were immediately dismissed by Republican lawmakers and others when they were made public this summer.

Within days, Austin issued an order saying he was canceling them. He said plea negotiations in possible death penalty cases related to one of the worst crimes ever committed on US soil were an important step that should be decided only by the defense secretary.

The judge had ruled that Austin did not have the legal authority to renege on the plea deals.

The pleas and Austin’s attempt to overturn them have been one of the most difficult episodes in a US prosecution marked by delays and legal difficulties. This includes years of pretrial hearings to determine the admissibility of defendants’ statements given their torture in CIA custody.

While the families of some of the victims and others are adamant that 9/11 prosecutions proceed to trial and possible death sentences, legal experts say it’s not clear that could ever happen. If the 9/11 cases ever clear trial hurdles, verdicts and sentences, the U.S. Court of Appeals for the District of Columbia Circuit would likely hear many of the issues in the course of any death penalty appeals.

Issues include the CIA’s destruction of interrogation videos, whether the rescinding of Austin’s plea deal constituted illegal interference, and whether the men’s torture tainted subsequent interrogations by “clean teams” of FBI agents that did not involve violence.