MANHATTAN (CN) - The chief judge of Guantanamo's military commissions system paused the prosecution against the alleged "mastermind" of the Sept. 11, 2001, attacks and his four accused accomplices, a newly unsealed order shows.
The ruling by Col. James Pohl, who presides over the 9/11 trial, condemns a controversial Pentagon order that would keep him and other Guantanamo judges in Cuba until they close their dockets.
Citing the need "to accelerate the pace of litigation," the convening authority of the military commissions system, retired Marine Corps Maj. Gen. Vaughn Ary, proposed that policy in a Dec. 9, 2014, memo to Deputy Secretary of Defense Robert Work.
When Work issued that change on Jan. 7 this year, defense attorneys for the 9/11 accused alleged that the policy was intended to pressure the judges to speed up litigation at the expense of due process.
From his 10-page order, it appears that Col. Pohl agreed.
"Unless the intent is to make the military judge ignore his duty to exercise discretion under the law and instead move the case faster to shorten his stay at GTMO, the purported change will not, and cannot, have its intended effect," Pohl wrote.
The rule change would mean an "objective, disinterested observer fully informed of all the facts and circumstances would harbor a significant doubt about the fairness of the proceeding," he added.
Appealing to an "independent trial judiciary," Pohl ordered the abatement of proceedings until the Pentagon rescinds the order.
Lt. Col. Myles Caggins, a Pentagon spokesman, indicated that the government may appeal the decision before proceedings continue in April.
"The government is studying the judge's ruling and will make an appropriate response through court filings," Caggins said in an email.
Pohl's order is sure to drag the already glacial proceedings of what has been called the largest criminal case in U.S. history.
It has been seven years since military prosecutors first charged Khalid Sheikh Mohammed, who once boasted of planning the 9/11 attacks from "A to Z," and his four alleged co-conspirators in Guantanamo Bay.
The men tried to plead guilty once before, but ironically, it was unclear whether the military commissions code would grant the death-penalty punishment that prosecutors wanted if the case did not go to trial.
President Barack Obama tried to transfer the men in New York, where their guilty pleas would have been quickly accepted in 2010.
His administration backed off a year later, however, in the face of political opposition, restarting proceedings in Guantanamo in late 2012.
Attorney James Connell, who represents alleged 9/11 financier Ammar al Baluchi, noted in a statement that the military commissions have been "plagued by intrusions by the FBI, CIA, and now senior DOD officials" over the past few years.
Col. Pohl once had to order a CIA censor out of the courtroom last year after finding an unknown agent cut off the audio feed during an unredacted portion of proceedings.
Defense attorneys alleged that government agencies snooped on their attorney-client meetings with a microphone disguised as a fire alarm, planted an informant on their legal team, and had access to their privileged emails.
Earlier this month, proceedings stumbled again when one of the men, Ramzi bin al Shibh, said that he recognized a linguist on the defense team from a CIA black site, the Miami Herald reported.
In a Jan. 30 legal brief, Connell said that the new order leaving Guantanamo judges in Cuba smacked of "unlawful command influence," the "mortal enemy of military justice."
His military co-counsel, Lt. Col. Sterling Thomas that the phenomenon had "no direct analogue in the civilian courts."
Connell added: "It would not surprise me if the administration seizes on this latest problem as an excuse to move the cases back to the civilian courts."
A spokeswoman for the White House's National Security Council did not immediately respond to a request for comment.
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