In a surprising turn of events, the military-run hearings for Khalid Sheikh Mohammed, the accused mastermind of the 9/11 attacks, and his two co-defendants at Guantanamo Bay have been thrown into turmoil following Defense Secretary Lloyd Austin's decision to reject a previously approved plea agreement.

Defense attorneys argue that the plea deal still stands and have suspended their participation in the pre-trial hearings while legal challenges to Austin's action unfold. Prosecutors also raised concerns that the hearings may have to be halted as lawyers grapple with the issues raised by Austin's order.

The presiding judge, Air Force Col. Matthew McCall, acknowledged the mounting external pressure on the case. The plea agreement, which aimed to spare the defendants from the death penalty, and Austin's subsequent order have elicited strong reactions, including from the families of the September 11 victims. The Biden administration has faced criticism, particularly from Republicans, over the plea deal.

Despite the potential for political pressure, Judge McCall stated during the hearing that it would not impact his decision-making process. Reporters were able to monitor the proceedings from Fort Meade, Maryland.

These recent developments mark yet another significant setback in the U.S. military's prosecution of the 9/11 defendants. The military commission responsible for trying the individuals involved in the 2001 attacks has faced considerable challenges due to unusual restrictions and legal complexities surrounding the case.

One of the key challenges has been addressing the issue of torture, as the defendants were subjected to mistreatment while in CIA custody. Consequently, the commission is still grappling with legal questions regarding the impact of torture on the admissibility of evidence.

The chain of events began unfolding after Susan Escallier, the chief authority over the Guantanamo Bay military commission, approved the plea agreement between the military-appointed prosecutors and defense attorneys. However, Defense Secretary Austin's order last Friday overrode Escallier's decision and asserted his direct control over such matters in the 9/11 case, citing its significance.

This move by Austin has sparked controversy, with defense lawyers and legal analysts questioning whether the laws governing the Guantanamo proceedings allow for such overruling. Some believe that Republican criticism of the plea deal, as well as pressure from certain victims' families, may have influenced Austin's decision.

Austin, however, emphasized the gravity of the losses suffered in the 9/11 attacks and the subsequent years of U.S. military intervention as the driving force behind his determination to proceed with the trials.

During Wednesday's hearing, defense attorneys asserted that they consider the plea bargain to still be in effect. Judge McCall agreed to excuse them from the pre-trial hearings while anticipated challenges to Austin's actions play out. Gary Sowards, the lead attorney for Khalid Sheikh Mohammed, informed the court that this process alone may take up to two years, further prolonging an already protracted case.

Walter Ruiz, an attorney representing defendant Mustafa al Hawsawi, condemned the defense chief's order as an unprecedented act that raises concerns about unlawful interference at the highest levels of government. He questioned the ethical implications of continuing to engage in the Pentagon-run commission, as this action strikes at the heart of the system's integrity.

Under the now-disputed plea agreement, Mohammed, Hawsawi, and fellow defendant Walid bin Attash would have entered guilty pleas, thereby avoiding the death penalty. Defense attorneys emphasized that the agreement would have obligated the accused to answer any remaining questions from victims' families and others about the attack.

Despite the tumultuous start, the hearing proceeded with the questioning of an FBI witness, with only one defendant, Aamar al Baluchi, actively participating in the defense.

The situation surrounding the military proceedings in the 9/11 case remains uncertain, further complicating an already lengthy and complex legal saga. As legal challenges continue, the fate of those accused in the horrific 2001 attacks remains in limbo.