In the aftermath of the September 11 attacks, the Bush administration sought "a tough-minded alternative to the civilian court system" for dealing with terrorists. President Bush asserted that the U.S. Constitution and a congressional resolution passed after the attack empowered him to promulgate the order as president. The order provided the authority for the Secretary of Defense to detain members of Al Qaeda at Guantanamo Bay detention camp.

Critics pointed out that, as of March 2006, none of the cases for the 10 terrorists designated for trial under the order had been concluded. They also argued that the suspects were tried for crimes defined by the President, using procedures "lacking basic protections", by judges who were subordinates of the President. Ultimately the commissions were modified to require that trials be public and defendants be assumed innocent until proven guilty beyond a reasonable doubt. However critics continued to argue that the Geneva Convention required the detainees to be tried in federal court with habeas corpus. The Bush administration countered that Al Qaeda is a terrorist network that has not signed the Geneva Convention and does not abide by it.^[2]

US District Court Justice James Robertson ruled, in Hamdan v. Rumsfeld, that the military commissions were unconstitutional. A three-judge appeals panel overturned Robertson's ruling. President Bush appointed John Roberts, one of the judges on that panel, to the vacant post of Chief Justice of the United States on the next business day. Justice John Roberts had to recuse himself when the appeal appeared before the United States Supreme Court. On June 29, 2006, the Supreme Court upheld Robertson's initial ruling 5–3. That ruling was later superseded by the Military Commissions Act of 2006.

Charlie Savage points to a more legalized understanding of which individuals could be detained under the Authorization for Use of Military Force under the Obama administration. He states that the standard became known as the "March 13 standard."^[3] It is in reference to a memorandum regarding the United States Government's detention of detainees held at Guantanamo Bay detention camp.^[4]

The standard put forth in the memo for determining whether an individual could be detained (outside of those individuals directly tied into the September 11 attacks) is if the person:

• Was part of or
  • the Taliban or
  • al-Qaida forces or
  • associated forces that are engaged in hostilities against the United States or its coalition partners, including any person who has committed a belligerent act, or has directly supported hostilities, in aid of such enemy armed forces; or
• Substantially supported
  • the Taliban or
  • al-Qaida forces or
  • associated forces that are engaged in hostilities against the United States or its coalition partners, including any person who has committed a belligerent act, or has directly supported hostilities, in aid of such enemy armed forces.^[5]