The U.S. Supreme Court case Salim Ahmed Hamdan v. Donald H. Rumsfeld, Secretary of Defense, et al., 2005 centered around the legality of military commissions set up by the Bush administration to try detainees at Guantanamo Bay. The plaintiff was Salim Ahmed Hamdan, a Yemeni national who had been Osama Bin Laden's driver and bodyguard and was captured in Afghanistan in 2001. He challenged his detention and trial by these military commissions on several grounds including that they violated both U.S law (Uniform Code of Military Justice) and international law (Geneva Conventions). In a landmark decision, the Supreme Court ruled in favor of Hamdan stating that these military commissions lacked "the power to proceed because its structures and procedures violate both the Uniform Code of Military Justice (UCMJ) and Geneva Conventions". This ruling significantly limited executive power during wartime operations.

In the dissenting opinion for Salim Ahmed Hamdan v. Donald H. Rumsfeld, Secretary of Defense, et al., Justice Clarence Thomas argued that the court's majority had overstepped its authority by intervening in military affairs during a time of war. He contended that it was not within their purview to question or interfere with the President’s decision on how to handle enemy combatants and detainees at Guantanamo Bay as this is an executive function under Article II of the Constitution. Furthermore, he disagreed with the majority's interpretation of Common Article 3 of Geneva Conventions arguing that it does not apply to Al Qaeda members since they are part of a non-state actor group engaged in terrorism rather than traditional warfare between nations. Additionally, he believed that Congress had implicitly authorized such tribunals when it passed Authorization for Use Military Force after September 11 attacks which gave president broad powers to deal with those responsible for them.