On November 13, 2001, President Bush issued a Military Order authorizing military commissions to try suspected terrorists who were not American citizens.
The Department of Defense then issued implementing orders:
The Military Order generated enormous opposition and initiated unending controversy over the proper role, if any, of military commissions in the war against al-Qa'ida. Below are some of the earlier critiques:
After the Supreme Court’s 2004 opinions rejecting by and large the Bush administration’s overly broad claims of detention authority and efforts to prevent any judicial review, the administration and the Congress adopted a series of measures on military commissions and detentions, each one of which generated new controversy and legal challenges.
The government’s argument that Congress had stripped Guantanamo detainees of habeas rights when it passed The Detainee Treatment Act of 2005 was rejected by the Supreme Court in 2006 in Hamdan v. Rumsfeld, 548 U.S. 557 (2006). CNSS had filed an amicus brief urging this result. Habeas petitions are one avenue for challenging military commissions. In Hamdan, the Court also rejected the military commissions set up by the Bush Administration because they did not comply with either the Geneva Conventions or the Uniform Code of Military Justice.
With the agreement of the administration, Congress then passed the Military Commissions Act of 2006. In Boumediene v. Bush, 553 U.S. 723 (2008) the Supreme Court held that the Act was an attempt to unconstitutionally suspend the writ of habeas corpus. It did not rule on the new military commissions and proceedings against several Guantanamo inmates were begun.
When the Obama administration took office, it initially suspended all military commission proceedings. It issued new rules providing defendants with greater due process protections. It then asked Congress for amendments to address other flaws in the system, which were adopted in the Military Commissions Act of 2009.
A few individuals have now been prosecuted in the commissions. The mastermind of the 9/11 attacks, Khalid Sheik Mohammed, is now facing trial by military commission along with others detained at Guantanamo. Legal challenges to the commissions are ongoing and have not been resolved.
For more information on the controversies and changes in the authorities for military commissions, see the Department of Defense website on military commissions.