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Guantánamo Bay — During one of many contentious exchanges at a recent pre-trial hearing in Guantánamo Bay for the five alleged masterminds of the 9/11 attack, defense attorney Derek Poteet argued that for a government agency to use its classification powers to cover up a crime is itself a crime. He was referring to the CIA’s black site program, much of which is still classified, and the torture his client, accused 9/11-mastermind Khalid Sheikh Mohammed, underwent in CIA custody. Poteet — a US Marine major — praised a 2006 government investigation into atrocities committed by US soldiers in Mahmudiyah, Iraq, arguing that even though the criminal proceedings sparked anti-US sentiment, burying the case in the name of national security would have been a mistake.

Military lawyer Robert Swann, arguing on behalf of the government, responded by offering the most straightforward and unabashed defense of the CIA’s program that has been made to date in the 9/11 case, to my knowledge. “Despite what one might think, I think and I know that lives were saved, and I sleep comfortably because of the very people that counsel impugned,” Swann said.

It was a stunning claim to make, and although Swann was speaking in a remote island courtroom inaccessible to nearly every US citizen, his comments could be a hint at what Trump’s election could mean not only for the future of the 9/11 trial, but also for US foreign policy more broadly. Following the revelations that the CIA tortured prisoners captured in the war on terror, and that the military carried out brutal detention practices at Abu Ghraib and other wartime prisons, the public largely turned against the euphemistically named “enhanced interrogation techniques.” By the time Obama was elected, most high-ranking national security officials had come to see the CIA’s black site program as a low point in the country’s foreign policy history.

Now, as President-elect Donald Trump prepares to take office, torture is making a bit of a comeback. Trump has repeatedly pledged to restart torture policies. James Mitchell, one of the two principle architects of the CIA program, recently released a memoir purporting to describe his experience interrogating high-value detainees, including Khalid Sheikh Mohammed. In a glowing review of Mitchell’s book, Washington Post columnist Marc Thiessen wrote, “Mitchell is an American patriot who has been unjustly persecuted for his role in crafting an interrogation program that helped stop terrorist attacks and saved countless lives.” Mitchell recently spoke at a gathering of Washington, DC, insiders, where he continued to defend his legacy of waterboarding, rectal feeding, sleep deprivation and other interrogation techniques.

The Thiessen piece was published about a week before Swann’s comments at Guantánamo Bay. Although it’s certainly possible that the similar wording is a coincidence, it’s worth remembering that for many in the greater US national security apparatus, the appropriateness of torture remains an open question. The shifting debate could have vast ramifications on the 9/11 case. It could influence everything from the opinions that jury members have on previous CIA practices, to whether or not the Senate’s torture report is preserved and made available as evidence should the case make it to trial.

Of the dozen or so motions taken up during a recent pre-trial hearing in the 9/11 case at Guantánamo Bay, the issue of torture was never far from anybody’s lips. The case is still in the pre-trial phase, as defense attorneys and the government argue endlessly over motions that have stretched out for years. The delay is due to the novel legal system the government is using to try the defendants, called military commissions, which borrows elements both from regular federal courts and from courts martial. Since the commissions are new — Congress passed the Military Commissions Act in 2006, and then updated the law in 2009 — all the interested parties have to litigate basic process issues like rules of evidence and protection against hearsay before the trial can start.

One key issue was whether or not the Trump administration, with the help of Senate Select Intelligence Committee (SSCI) Chair Richard Burr, would attempt to destroy the Senate’s 6,700-page torture report. The full report remains classified, and Burr has demanded that all executive branch copies of the report be returned to his committee. Sen. Diane Feinstein, the previous head of the committee, distributed copies of the report to the heads of the Department of Defense (DOD), the Department of State and the Department of Justice, as well as to the intelligence committee. The copy given to the CIA’s inspector general was reportedly inadvertently destroyed, something the defense teams are worried could happen to every existing copy. (Obama has since promised to retain at least one copy in his presidential library, though it will remain hidden from the public for at least 12 years.)

To prevent the total destruction of the report, the defense teams asked the judge in the 9/11 case, retired Army Col. James Pohl, to demand the government provide him with a copy of the full report under seal. The government objected to that defense motion. Its official position, in the wake of Burr’s demand that all executive branch copies be returned to his committee, was that “the United States Department of Defense can nonetheless assure the commission that it will preserve the status quo regarding the full SSCI report.”

Here, too, Trump’s election threatens to fundamentally alter the 9/11 trial. “The new administration has made statements promising waterboarding or worse, and there are many reasons to believe that it is hostile to [the] preservation of the report,” defense attorney James Connell said during the hearing. “Since both the legislature and the executive will be under control of persons who have expressed their displeasure with the report, there is a real reason to suspect that the report could be destroyed either inadvertently, as [by the] CIA Inspector General, or as part of a political strategy.”

Because of those threats, Connell argued that the promise to “preserve the status quo” was vague and insufficient. He asked Judge Pohl to determine whether or not the Pentagon still had its copy of the full report, that is, what exactly the government meant by the “status quo.” The judge asked Chief Prosecutor Gen. Mark Martins for his position, at which point the ensuing back-and-forth took on the flavor of absurdist theater.

The prosecution’s argument is that although the DOD was given a copy, the report belongs solely to the legislative branch. “We have been reviewing [the report] in spaces in the Senate,” Gen. Martins told the judge.

“When you said in February that the Department of Defense maintained the status quo, does that

mean the Department of Defense still has a copy of it, to your knowledge?” Judge Pohl asked.

“We are reviewing the original document,” Gen. Martins responded, referring to the Senate’s copy, not the DOD’s. Judge Pohl continued to press for clarification as to whether Connell’s argument was already moot — that is, whether the DOD copy still existed or not. “And I’m not prepared to tell you,” Martins said.

Judge Pohl wasn’t satisfied: “But you can tell me you can go back to the Department of Defense and say do you have a copy?” Gen. Martins didn’t give an inch. “Your Honor, it’s a legislative copy,” he reiterated.

After one more back and forth, Judge Pohl delivered one of his trademark understatements, revealing his growing exasperation. “General Martins, the government sometimes makes this stuff much more difficult than it needs to be,” he deadpanned.

With the inauguration looming on the horizon, the five defense teams asked the judge to expedite his ruling on the motion, and Judge Pohl issued an order that afternoon compelling the government to tell him by December 16 whether the DOD still has a copy of the full report.

When I asked Gen. Martins at the press conference at the end of the week if he knew whether DOD’s copy had been preserved, he directed me to the judge’s order.

It’s unlikely that the 9/11 trial will be high on President Trump’s list of priorities, for now at least. The trial is at least a year away, and Trump, famously known for his inability to concentrate on details, would likely have a hard time getting brought up to speed on arguably the most complicated investigation and trial in the history of the United States. Still, his administration could exert considerable sway over the proceedings, not least of all because the military commissions process itself is so new and subject to constant creation and revision.

In other words, under the Trump administration, a trial that has already been marred by delay and controversy is only going to face further obstacles before it is finally resolved.