The judges also voided an order issued by Spath that sought to require two defense attorneys for the defendant, Abd al-Rahim al-Nashiri, to return to the case against their will.

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The ruling is the latest blemish for the troubled commissions set up in the wake of the Sept. 11, 2001, attacks to try prisoners held at Guantanamo Bay, Cuba. Of a once-vast detainee population there, only 40 inmates remain. Nearly two decades after the attacks, the start of the trial of 9/11 suspects remains far off amid seemingly endless legal wrangling and procedural delays.

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The decision also suggests that federal courts may no longer be as deferential to the war courts and to the larger Guantanamo system as they have been in the past, as commission proceedings drag on for years and some two dozen other detainees languish without the suggestion of a trial.

Nashiri, a Saudi national in his 50s, faces a possible death penalty for his alleged orchestration of a string of plots to bomb Western vessels, including the Cole attack, which killed 17 Americans. After his capture, Nashiri was subject to extensive torture in CIA custody.

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“Many years ago, when Abd al-Rahim first heard he was being handed over to the Americans, he was actually happy because he thought the United States was a country of laws and rights and that he’d at least be treated fairly,” said Navy Lt. Alaric Piette, a member of Nashiri’s defense team. “Finally, after 16 years, with this ruling, that has actually happened. Which is to say that this will mean a lot to him.”

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Spath, who recently retired as an Air Force colonel, suspended Nashiri’s case in early 2018 over a dispute with defense lawyers who resigned after finding a microphone in a room used for attorney-client discussions. The judge’s order that the attorneys remain on the case kicked off a complex controversy involving several legal bodies and resulted in the house arrest of a brigadier general tasked with overseeing commission defense teams.

A year into his involvement in the case, Spath meanwhile quietly applied to the Justice Department for a position as an immigration judge. Such judges are appointed by the attorney general.

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The D.C. Circuit judges, in a stinging rebuke, responded this week by throwing out rulings in the case from the commission and at least some from its appeals body, beginning at the moment when Spath initiated his job application in November 2015.

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“Although a principle so basic to our system of laws should go without saying, we nonetheless feel compelled to restate it plainly here: criminal justice is a shared responsibility,” Judge David Tatel wrote in the panel’s ruling. “Yet in this case, save for Al-Nashiri’s defense counsel, all elements of the military commission system — from the prosecution team to the Justice Department to the CMCR [U.S. Court of Military Commission Review] to the judge himself — failed to live up to that responsibility.”

“This much is clear: whenever and however military judges are assigned, rehired, and reviewed, they must always maintain the appearance of impartiality,” Tatel wrote.

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The CMCR is the Guantanamo appeals body. Tatel was joined on the panel by Judges Judith Rogers and Thomas Griffith.

Michael Paradis, an attorney who represented Nashiri in the D.C. Circuit case, said the opinion revealed the judges’ frustration “that the system is cavalier about such basic roles and so broken as a consequence. The whole thing has become so shambolic.”

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In a striking insight into the court’s thinking, the decision appeared to suggest that the judges considered what Tatel described as a “powerful case for dissolving the current military commission entirely” — that is, they examined the possibility of voiding the entire Nashiri case to date. Such a move would strike an even more massive blow to the military justice architecture of the post-9/11 era.

The government could appeal the ruling. A spokeswoman for the Justice Department declined to comment on pending litigation.

Spath’s successor on the military court also left to become an immigration judge.