WASHINGTON (AP) — A U.S. military judge at Guantanamo Bay, Cuba, has scheduled hearings in early January for alleged 9/11 mastermind Khalid Sheikh Mohammed and two co-defendants to enter guilty pleas in exchange for life sentences despite Defense Secretary Lloyd Austin’s effort to scuttle the plea agreements.

The move Wednesday by Judge Matthew McCall, an Air Force colonel, in the government’s long-running prosecution in the Sept. 11, 2001, attacks that killed nearly 3,000 people signals a deepening battle over the independence of the military commission at the naval base at Guantanamo.

McCall provisionally scheduled the plea hearings to take place over two weeks starting Jan. 6, with Mohammed — the defendant accused of coming up with using commercial jetliners for the attacks — expected to enter his plea first, if Austin’s efforts to block it fails.

Austin is seeking to throw out the agreements for Mohammed and fellow defendants Walid bin Attash and Mustafa al-Hawsawi, which would put the more than 20-year government prosecution efforts back on track for a trial that carries the risk of the death penalty.

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While government prosecutors negotiated the plea agreements under Defense Department auspices over more than two years, and they received the needed approval this summer from the senior official overseeing the Guantanamo prosecutions, the deals triggered angry condemnation from Sens. Mitch McConnell and Tom Cotton and other leading Republicans when the news emerged.

Within days, Austin issued an order throwing out the deals, saying the gravity of the 9/11 attacks meant any decision on waiving the possibility of execution for the defendants should be made by him.

Defense attorneys argued that Austin had no legal standing to intervene and his move amounted to outside interference that could throw into question the legal validity of the proceedings at Guantanamo.

U.S. officials created the hybrid military commission, governed by a mix of civilian and military law and rules, to try people arrested in what the George W. Bush administration called its “war on terror” after the 9/11 attacks.

The al-Qaida assault was among the most damaging and deadly on the U.S. in its history. Hijackers commandeered four passenger airliners and flew them into the World Trade Center and the Pentagon, with the fourth coming down in a field in Pennsylvania.

McCall ruled last week that Austin lacked any legal ground to reject the plea deals and that his intervention was too late because it came after approval by the top official at Guantanamo made them valid.

McCall’s ruling also confirmed that the government and Guantanamo’s top authority agreed to clauses in the plea deals for Mohammed and one other defendant that bar authorities from seeking possible death penalties again even if the plea deals were later discarded for some reason. The clauses appeared written in advance to try to address the kind of battle now taking place.

The Defense Department notified families Friday that it would keep fighting the plea deals. Officials intended to block the defendants from entering their pleas as well as challenge the agreements and McCall’s ruling before a U.S. court of military commission review, they said in a letter to families of 9/11 victims.

The Pentagon on Wednesday did not immediately answer questions on whether it had filed its appeal.

While families of some of the victims and others are adamant that the 9/11 prosecutions continue to trial and possible death sentences, legal experts say it is not clear that could ever happen. If the 9/11 cases clear the hurdles of trial, verdicts and sentencings, 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.

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