The court moves in this direction by effectively reading al-Qaida into the Geneva Conventions. The conventions are a treaty to which nations voluntarily bind themselves. Al-Qaida has never signed on, since 1) it isn't a nation; and 2) it would be an obstacle to practices that are central to its organization, including slaughtering civilians and beheading prisoners. But the court bestows a bonus membership to al-Qaida, because it furthers the court's goal of dictating how captured al-Qaida members should be tried.
It's not that the court's reading of the Geneva Conventions is entirely implausible, but that the president has another, more reasonable reading of Geneva that there is no reason for the court to trample on. But trample it does, a quality of its decision throughout.
Justice Clarence Thomas writes in dissent, "Those Justices who today disregard the commander-in-chief's wartime decisions, only 10 days ago deferred to the judgment of the Corps of Engineers with regard to a matter much more within the competence of lawyers, upholding that agency's wildly implausible conclusions that a storm drain is a tributary of the water of the United States. It goes without saying that there is much more at stake here than storm drains."
From its conclusion that Geneva applies to al-Qaida, the court works its way toward mandating that military commissions must duplicate the structure of courts-martial. This in itself needn't be disastrous, but the court is on a dangerous path. The decision sets the table for more severe judicial interference in the war-making of the executive branch and Congress. Justice Stevens surely has many impressive talents, but fighting al-Qaida isn't one of them.
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