FORT MEADE, Md. (AP) — Military-run hearings for accused Sept. 11 mastermind Khalid Sheikh Mohammed and two co-defendants at Guantanamo Bay, Cuba, were in upheaval Wednesday following Defense Secretary Lloyd Austin’s decision to throw out a plea agreement.

Defense attorneys contend the plea deal still stands and suspended participation in the pre-trial hearings while legal challenges to Austin’s action play out. Prosecutors also raised the prospect that the pre-trial hearings might have to be frozen as lawyers look for explanations in Austin’s order and work through the issues raised by it.

The judge overseeing the case, Air Force Col. Matthew McCall, acknowledged concerns over outside pressure on the case. The plea agreement, which would have spared the defendants the risk of the death penalty, and Austin’s subsequent order, issued late Friday, have generated strong feelings, including among the families of Sept. 11 victims. The Biden administration came under heavy Republican criticism over the plea deal.

“If more political pressure is put on the parties to make a decision one way or the other,” that could build the case for illegal interference in the case, “but … it’s not going to affect me,” McCall said during Wednesday’s hearing. Reporters were able to monitor the proceedings from Fort Meade, Maryland.

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The events of the past week are the latest significant disruption of the U.S. military prosecution of defendants accused in the 2001 killings of nearly 3,000 people, in an al-Qaida plot that saw hijackers commandeer four passenger airliners and fly them into the World Trade Center and the Pentagon, with the fourth coming down in a field in Pennsylvania.

Set up as former President George W. Bush and his Defense Secretary Donald Rumsfeld pursued what they called the U.S. war on terror, the military commission trying the 9/11 defendants has struggled with some of the unusual restrictions and legal challenges of the case.

That includes the torture of the defendants while in CIA custody in their first years after being captured, leaving the commission still hammering out legal questions over the effect of the torture on evidence.

The new developments began unfolding last week after the Pentagon-approved chief authority over the Guantanamo Bay military commission, Susan Escallier, approved the plea agreement between the military-appointed prosecutors and defense attorneys, which had been two years in the making.

Austin said in Friday’s order that he was overriding Escallier’s approval and taking direct control of such decisions in the 9/11 case going forward. He cited the significance of the case.

Defense lawyers and some legal analysts are challenging whether the laws governing the Guantanamo proceedings allow for that overruling.

Some of the attorneys and rights groups charge that the Republican criticism of the plea deal, and criticism from some of the families of the victims, appear to have influenced Austin’s action. Austin told reporters on Tuesday that the gravity of the American losses in the al-Qaida attack and in the years of U.S. military intervention that followed convinced him that the cases had to go to trial.

Defense attorneys told McCall on Wednesday they considered the plea bargain still in effect. McCall agreed to excuse them from participating in the pre-trial hearings while expected challenges to Austin’s actions play out.

Gary Sowards, the lead attorney for Mohammed, the accused mastermind of the 9/11 attacks, warned the court on Wednesday that that process alone was likely to take up to two year, adding to the length of a troubled case already well into its second decade.

“To intervene in this most unusual way ensures total chaos from this point forward,” Sowards told McCall, referring to Austin’s action.

Walter Ruiz, an attorney for 9/11 defendant Mustafa al Hawsawi, called Austin’s order “an unprecedented act by a government official to pull back a valid agreement” and said it raises issues involving “unlawful interference at the highest levels of government.”

Ruiz said the defense chief’s move also raised questions “whether we can ethically continue to engage” in the Pentagon-run commission in the face of an action “that goes right at the heart of the integrity of the system itself.”

Under the plea agreement, Mohammed, Hawsawi, and fellow defendant Walid bin Attash would have entered guilty pleas in exchange for the government not seeking the death penalty against them. Defense attorneys stressed Wednesday the agreement would have committed the accused to answer any lingering questions about the attack from family members of victims and others.

After Wednesday’s tumultuous start, the hearing proceeded with the questioning of an FBI witness, with the active defense participation of only one defendant who had not taken the plea agreement, Aamar al Baluchi.

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