A military judge indefinitely halted a death-penalty case Friday linked to the 2000 bombing of the USS Cole, dealing a significant blow to the already troubled military court system for terrorism suspects at Guantanamo Bay.

The decision by Air Force Col. Vance Spath, who voiced exasperation at what he characterized as repeated defiance of his authority by defense attorneys, is a striking illustration of the deep-rooted problems plaguing the judicial process set up in the wake of the Sept. 11, 2001, attacks.

More than 16 years later, trials for 9/11 suspects are still stuck in pretrial proceedings, and conclusions remain years away. Of the more than 700 inmates held at the military prison in Cuba since 2002, only a handful have been successfully tried. About half the remaining 41 prisoners are expected to be held indefinitely without charge.

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“This is another wake-up call, and a dramatic one, because the issues go again to the fundamental legitimacy of the commissions,” said Hina Shamsi, director of the American Civil Liberties Union’s national security project.

The suspension caps a succession of crises facing the Guantanamo commissions in recent months, including the resignation of civilian lawyers for the accused Cole mastermind, Abd al-Rahim al-Nashiri; a contempt ruling against a general overseeing defense teams; and the firing — without explanation — this month of senior Pentagon officials overseeing the courts.

“If that’s not the wheels coming off, I don’t know what is,” said Rita Siemion, international legal counsel at Human Rights First.

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The growing sense of disarray comes as the Trump administration considers bringing new terrorism suspects to Guantanamo Bay for the first time in a decade, instead of seeking to try them in federal courts, raising the possibility of new protracted legal sagas.

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Past problems that have haunted the commissions’ credibility include the torture of terrorism suspects at overseas prison sites, microphones hidden in attorney-client meeting rooms at Guantanamo and a “kill switch” that unknown officials used to mute court proceedings.

Hours after Spath’s announcement, Cmdr. Sarah Higgins, a Pentagon spokeswoman, said the government was “studying transcripts from this week in which the judge made important findings and rulings.”

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“It is unknown when pretrial hearings will begin again,” she said in an email.

The suspension prolongs years of anticipation for the families of the 17 Americans who were killed in the Cole attack, in which militants blew a hole in the ship’s hull while it was stopped off the coast of Yemen in October 2000.

Spath, in a lengthy statement delivered during pretrial proceedings Friday, focused his displeasure on the defense team representing Nashiri. Only one lawyer, Lt. Alaric Piette, remains on that team after civilian defense attorneys resigned last fall, arguing that they could not ethically continue to represent their client, in what appeared to be a response to possible government interference in attorney-client communications.

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That crisis was compounded when Spath held Brig. Gen. John G. Baker, the chief defense counsel for the commissions, in contempt and ordered him confined to quarters when he supported the lawyers’ departure.

Spath’s frustration mounted when two of Nashiri’s former lawyers, Rosa Eliades and Mary Spears, did not obey his orders to appear in court via video and as Piette, a relatively junior attorney, argued that he could not proceed without a co-counsel experienced in capital cases.

The confusion was compounded this month when Defense Secretary Jim Mattis fired Harvey Rishikof, responsible for overseeing the military court, without explanation. Another official, Gary Brown, was also fired.

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While it is unclear if their dismissals were related to the Nashiri case, Rishikof had circulated a memo several months earlier seeking a way forward on that case, making reference to a need to create a “clean facility” that would protect attorney-client communications.

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Speaking Friday, Spath said the recent events had “demonstrated significant flaws within the commission process, particularly within the defense organization, and it demonstrates an organization intent on stopping the system.”

“What they’re doing is engaging in revolution to the system,” he said, according to a transcript provided by the Pentagon. “It’s shaken me more than I would have expected.”

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The judge said the case would remain suspended “until a superior court orders me to resume.” It is not clear whether the Court of Military Commission Review or the D.C. District Court — or possibly another court — might intervene.

Stephen Vladeck, a professor at the University of Texas School of Law, said the suspension was unlikely to affect the commissions’ three other active cases.

“This is just the latest of many flash points that all point in the same direction — that there are potentially insurmountable roadblocks to trying these cases the way the government wants to try them,” Vladeck said.

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Richard Kammen, a veteran death-penalty attorney who was among the Nashiri lawyers who resigned last fall, said he believed that his former client could be tried by a civilian judge in a year to 18 months.

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“Maybe somebody will take a step back and realize that the best place for Mr. al-Nashiri’s case, and the 9/11 case as well, is in a federal court,” Kammen said.

According to Michel Paradis, Nashiri’s Pentagon-appointed appellate lawyer, Nashiri’s case was abated previously in 2015 while the Court of Military Commission Review reviewed several measures. He said Spath’s decision was different.

“He’s basically saying this case has become a dumpster fire,” he said. “The good news I think is that Colonel Spath finally came around and realized this dumpster fire could not keep going.”

Spath, closing court proceedings, told the court that he would decide in coming weeks whether to retire.

CORRECTION: A previous version of this article misstated when the USS Cole bombing took place. The attack occurred in October, not August, 2000.

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