Initially, the Department of Defense sought to try detainees as war criminals through military commissions as opposed to the courts-martial mandated under the arguing the military commissions lacked jurisdiction and violated the Geneva Conventions. In August 2005, Commission Order No. 1 [PDF] revised and delineated commission procedures, and later that year Congress passed the Detainee Treatment Act of 2005, which placed limitations on the jurisdiction of federal courts in reviewing the military commissions. In June 2006, however, the US Supreme Court ruled in Hamdan v. Rumsfeld that the government lacked the authority to establish the commissions because they failed to comply with Article 36 of the UMCJ by unjustifiably deviated from the rules for courts-martial. The court also found that the commissions failed to comply with Article 3 of the Geneva Conventions.
Congress responded to the court's decision in Hamdan by quickly passing the Military Commissions Act of 2006 (MCA), which established the current military commissions system and removed jurisdiction from every "court, justice, or judge ... to hear or consider an application for writ of habeas corpus filed by ... an alien ... detained as an enemy combatant." In Boumediene v. Bush, the US Supreme Court overturned MCA provisions stripping federal courts of habeas corpus jurisdiction, finding that detainees at Guantanamo must have habeas corpus rights under the US Constitution. In October 2008, the US District Court for the District of Columbia adopted the definition of enemy combatant provided in a 2004 Order Establishing Combatant Status Review Tribunal [PDF], meaning detainees must have directly supported hostilities against the US or its allies. Finally, in March 2009, the US Department of Justice (DOJ) dropped the term "enemy combatant" from its legal lexicon and established a new criterion for detention that "does not rely on the President's authority as Commander-in-Chief independent of Congress's specific authorization" under the Authorization for the Use of Military Force passed by Congress in September 2001.
However, conflict over the legal status of detainees abroad continues. In May 2010, the US Court of Appeals for the District of Columbia Circuit ruled that Boumediene only applied to detainees being held at Guantanamo and that detainees held at Bagram Air Force Base in Afghanistan cannot bring habeas corpus challenges in federal courts.