Last week’s ruling in Boumediene v. Bush was, as one legal scholar put it shortly after the decision was released, “a stunning blow to the Bush administration.” The ruling, however, should not have come as a surprise to the administration or its critics.

The Supreme Court has been playing a bit of a game with the other two branches of government over this issue for years. In 2004, the Court ruled in Rasul v. Bush that the U.S. courts do have jurisdiction over what goes on at Guantanamo Bay. The key question in that case was whether the naval base at Guantanamo Bay was truly American territory or not. On that question, Justice Anthony M. Kennedy wrote in his concurring opinion:

What matters is the unchallenged and indefinite control that the United States has long exercised over Guantanamo Bay. From a practical perspective, the indefinite lease of Guantanamo Bay has produced a place that belongs to the United States, extending the “implied protection” of the United States to it.

The Court further ruled that the detainees had to be afforded the right to challenge their detention somehow (which is what is meant by habeas corpus rights). That ruling is what prompted Congress to pass the Military Commissions Act, which established a unique set of military tribunals at Guantanamo Bay that would hear the cases of the detainees held there. Those tribunals were not the equivalent of a normal military tribunal, which would be covered under the Uniform Code of Military Justice. The due process protections — safeguards that assure a fair and objective trial — were weaker than those required in a normal military trial, though there were some protections. But it was clear to most observers that if those tribunals did not provide enough protections for due process to satisfy the Supreme Court, the justices would likely intervene again. And so they have.

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Once those tribunals were set up and preparations begun for the first cases to be heard, it didn’t take long for serious problems with the process to come to the fore. Defense attorneys almost immediately asked the Supreme Court to hear a challenge to the validity of those tribunals, but the court denied that request. But then Col. Stephen Abraham, a highly decorated military intelligence officer and JAG (military judge advocate general) attorney who was called up from reserve duty to assist in these tribunals, went public with his criticisms of the tribunal procedures.

He told The New York Times that the cases against many of the detainees were based on little more than vague associations and intelligence reports that were “stripped down, watered down, removed of context, incomplete and missing essential information.” What disturbed him most, he said, was “the willingness to use very small fragments of information” as a basis for holding people indefinitely. Abraham, a conservative Republican, could not in good conscience contribute to what he believed was a miscarriage of justice. “It is my duty,” he said, to come forward and speak out publicly about this. After Abraham wrote a letter to the Supreme Court justices detailing his observations, the Court reversed itself and agreed to hear challenges to the tribunals themselves.

But Abraham was hardly alone. Soon after he came forward, so did Col. Morris Davis, an Air Force officer assigned to be the chief prosecutor for the Guantanamo tribunals. In October 2007, Davis resigned that position and wrote an op-ed piece in The Los Angeles Times explaining why. His first reason was the lack of independence for the prosecutorial staff:

In a nutshell, the convening authority is supposed to be objective — not predisposed for the prosecution or defense — and gets to make important decisions at various stages in the process. The convening authority decides which charges filed by the prosecution go to trial and which are dismissed, chooses who serves on the jury, decides whether to approve requests for experts and reassesses findings of guilt and sentences, among other things.

Earlier this year, Susan Crawford was appointed by the secretary of defense to replace Maj. Gen. John Altenburg as the convening authority. Altenburg’s staff had kept its distance from the prosecution to preserve its impartiality. Crawford, on the other hand, had her staff assessing evidence before the filing of charges, directing the prosecution’s pretrial preparation of cases (which began while I was on medical leave), drafting charges against those who were accused and assigning prosecutors to cases, among other things.

How can you direct someone to do something — use specific evidence to bring specific charges against a specific person at a specific time, for instance — and later make an impartial assessment of whether they behaved properly? Intermingling convening authority and prosecutor roles perpetuates the perception of a rigged process stacked against the accused.

He also objected to the fact that the tribunals put the consideration of nearly all the evidence behind closed doors, arguing that “even the most perfect trial in history will be viewed with skepticism if it is conducted behind closed doors. Telling the world, ‘Trust me, you would have been impressed if only you could have seen what we did in the courtroom’ will not bolster our standing as defenders of justice.” Lastly, he said, he resigned after he was placed in a chain of command under the authority of William Haynes, general counsel to the Pentagon, who had specifically authorized the use of waterboarding, whereas Davis had ordered his prosecutors not to use any evidence obtained through any form of torture.

Soon after he resigned as chief prosecutor, the Senate Judiciary Committee asked him to testify about what was going on at the Guantanamo tribunals. The Bush administration was so eager to keep the details out of public view that they ordered Davis not to testify, and since Davis was an active duty officer they had the authority to do so. Instead, they sent Brig. Gen. Thomas Hartmann, who supported the administration’s position on the issue.

The Supreme Court took the affidavits filed by these men seriously. These were not American Civil Liberties Union (ACLU) attorneys who could be dismissed as wild-eyed leftists; these were highly decorated military officers blowing the whistle on the Guantanamo proceedings. And in the end, the court ruled that the protections provided by those military tribunals were not enough. The detainees, they ruled, must be allowed to challenge their detention in a regular court with regular due process protections. Because these cases involve information that is classified, the hearings won’t be exactly like regular hearings, but they will likely be a lot closer than the military tribunals have been.

The Supreme Court said that all of the challenges by detainees would be heard by the federal D.C. circuit appeals court and the judges of that circuit are already meeting to work out a set of procedures for hearing the cases that will provide due process while respecting the sensitive nature of some of the evidence.