When passed, Congress intended the War Powers Resolution to halt the erosion of Congress's ability to participate in war-making decisions. The terrorist attacks against the World Trade Center on September 11, 2001, however, created new complications for the separation of powers within the war powers sphere. After September 11, the United States Congress passed the Authorization for Use of Military Force against Terrorists (AUMF). President George W. Bush and his cabinet invaded Afghanistan to root out the Taliban government, which ruled Afghanistan and permitted the Al Qaeda terrorist network to conduct terrorist training within the country's borders. During the conflict, the U.S. military rounded up alleged members of the Taliban and those fighting against U.S. forces. The military then placed these "detainees" at a U.S. base located at Guantanamo Bay, Cuba at the direction of the Bush Administration who designed the plan under the premise that federal court jurisdiction did not reach the base. Consequently, the Bush Administration and military believed that the detainees could not avail themselves of habeas corpus and certain protections guaranteed by the U.S. Constitution.
As the military held many of these prisoners at the base for years without bringing formal charges against them, the prisoners found counsel within the United States to file habeas corpus petitions within U.S. federal courts. A series of cases then came before the U.S. Supreme Court dealing with the constitutionality of the prisoners' detentions at Guantanamo.
In 2004 Rasul v. Bush became the first case in which the Supreme Court directly discussed the Bush Administration's policies. 542 U.S. 466. The Court in this case held that 28 U.S.C. § 2241 permits federal district courts to hear habeas corpus petitions by aliens held within territory over which the United States exercises "plenary and exclusive jurisdiction." This holding included Guantanamo detainees. The Court then instructed the district courts to hear the petitions.
After the Bush Administration responded to Rasul by permitting detainees to bring their petitions before military tribunals, the Supreme Court again addressed the matter in 2006 when they handed down Hamdan v. Rumsfeld. 548 U.S. 557. The Hamdan opinion held that the President lacks constitutional authority under the Commander in Chief Clause to try detainees in military tribunals. The tribunals also violated the Uniform Code of Military Justice and the Geneva Conventions. Furthermore, the Court rebuked the government's arguments that the AUMF expanded Presidential authority.
Congress responded by passing the Detainee Treatment Act, which provides that "no court, court, justice, or judge shall have jurisdiction to hear or consider . . . an application for a writ of habeas corpus filed by . . . an alien detained . . . at Guantanamo Bay, Cuba." Lakhdar Boumediene, an Algerian citizen, challenged the constitutionality of this statute in Boumediene v. Bush (06-1195) in 2008. The Court struck down the Bush Administration's policies for a third time, holding that a Congressional suspension of habeas corpus requires an explicit suspension of the writ and that merely stripping the federal courts of jurisdiction does not actually suspend the writ. The Court also argued that the detainees lacked proper procedural safeguards to ensure a fair trial and the ability to ascertain the nature of their charges.