NEW YORK — The United States’ long legal case against accused Sept. 11 mastermind Khalid Sheikh Mohammed remains in limbo after an appeals court this week scrapped a plea deal that the government had negotiated but had later withdrawn.

Essentially, the ruling leaves the case on track for trial before a military commission. It is unclear when that might happen.

Here’s what to know about the case and how it got here:

Mohammed is accused of developing and directing al-Qaida’s plot to crash hijacked airliners into the World Trade Center and the Pentagon on Sept. 11, 2001. Another of the hijacked planes flew into a field in Pennsylvania. In all, nearly 3,000 people were killed in one of the deadliest attacks ever on the United States.

Mohammed was arrested in 2003 in Pakistan and eventually taken to the U.S. military base at Guantánamo Bay, Cuba. At the time, it was where the U.S. held hundreds of men captured in President George W. Bush’s “war on terror.”

Military prosecutors filed charges in 2008 against Mohammed and some co-defendants. After an Obama-era plan to try them in a civilian court in New York collapsed, the case remained with the military commission.

The case dragged on through years of legal and logistical challenges. A major point of contention has been how much the evidence and case have been tainted by the men’s torture while in CIA custody during the first years after their capture. Mohammed was waterboarded 183 times.

Military prosecutors and defense lawyers began plea talks several years ago. Last year, Mohammed and two others agreed to plead guilty, under an agreement that would have led to life in prison instead of a potential death penalty. The deal also would have required the men to answer questions posed by Sept. 11 victims’ relatives.

Military prosecutors called the arrangement “the best path to finality and justice.” Some 9/11 families also saw the deal as the best hope for bringing the painful case to a conclusion and getting some answers from the defendants.

But other victims’ relatives said a trial was the right way to get justice and information, and some saw the plea deal as capitulation. Republican lawmakers also criticized the agreement, negotiated during Democratic President Joe Biden’s administration.

Then-Defense Secretary Lloyd Austin soon rescinded the deal, saying that victims’ relatives, U.S. troops and the American public “ deserve the opportunity ” to see military commission trials play out.

Defense attorneys and the government wrangled in various courts over whether Austin was legally able to scrap the deal. It was on-again, off-again for months. A panel of appeals judges put it on hold in January and then, on Friday, issued 2-1 ruling saying that Austin had the authority to rescind the agreement. The order bars the military judge from taking any guilty pleas under the now-undone deal.

It is not clear whether defense lawyers plan to appeal. A message seeking comment was sent Saturday to Mohammed’s attorneys.

Without a plea deal, the case would once again be back in the pretrial stage within the military commission system, with the legal and logistical complications that it has faced. Questions about whether the men’s torture would prevent the use of evidence, including statements they made, are yet to be resolved.

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