Decorations are left behind on the panel of names at the 9/11 memorial site in New York City on September 11, 2024.
CNN  — 

The US government plans to appeal a military judge’s ruling that plea deals with the alleged 9/11 conspirators at Guantanamo Bay — which were revoked by Defense Secretary Lloyd Austin — are valid, a defense official said Saturday.

The prosecution is expected to ask the judge, Col. Matthew McCall, to pause court proceedings, the official said, in order to file an appeal of the decision. The accused were expected to submit their guilty pleas as early as next week, after McCall ruled Wednesday that Austin acted too late when he revoked the plea deals, making them “valid and enforceable.”

The US reached a plea deal in July after more than two years of negotiations between the government and the alleged conspirators – Khalid Sheikh Mohammed, accused mastermind of the September 11, 2001, attacks, and plotters Walid Bin ‘Attash and Mustafa Ahmed Adam al Hawsawi. The deals would allow the men to avoid the death penalty by pleading guilty and being sentenced to life in prison. Prosecutors wrote in a letter at the time that the deals were “the best path to finality and justice in this case.”

Austin abruptly revoked the plea deals in August, arguing the responsibility for such a significant decision “should rest with me.” He also yanked responsibility from the convening authority for military commissions, who runs the military courts at Guantanamo.

The U.S. issued charges on April 4, 2012, against Khalid Sheikh Mohammed (file photo), along with four alleged plotters.

The plea deals faced bipartisan backlash from lawmakers and some groups representing 9/11 victims that have pushed for the US government to pursue the death penalty.

“While some may disagree, even in our own community, I don’t think the Biden admin should have worked to cut these deals in the first place,” Brett Eagleson, president of 9/11 Justice, said in a statement provided to CNN earlier this week. “It doesn’t do a single thing to ease our pain [or] bring us closure. Nobody has listened to what we actually want/need and that is closure.”

Meanwhile, the American Civil Liberties Union lauded Wednesday’s ruling, saying it allowed the case to move forward.

“As a nation, we must move forward with the plea process and a sentencing hearing that is intended to give victim family members answers to their questions,” ACLU Executive Director Anthony Romero said in a statement. “They deserve transparency and finality about the events that claimed their loved ones.”

The case has been stalled over the course of the two decades since Mohammed’s capture in Pakistan in 2003 for his alleged involvement in the terror attacks. The US for years tried to determine how to handle the issue of torture used against Mohammed and others at secret CIA prisons in the 2000s, which delayed the military trial. The issue posed a legal problem for prosecutors about whether evidence obtained through torture was admissible in court.

The trial was set to begin on January 11, 2021, but delays brought about by the resignation of two judges and the Covid-19 pandemic pushed the date back again. Negotiations over the plea deals began in March 2022.

CNN’s Kaanita Iyer, Oren Liebermann, Lauren del Valle and Evan Perez contributed to this report.