The case of Boumediene et al. v. Bush was brought to the United States Court of Appeals for the District of Columbia Circuit. The court ruled that aliens designated as enemy combatants and detained at Guantanamo Bay have the constitutional privilege of habeas corpus. However, the court dismissed the cases for lack of jurisdiction due to Guantanamo being outside the sovereign territory of the United States. Congress passed the Detainee Treatment Act of 2005 and the Military Commissions Act of 2006, which amended §2241 to prohibit courts from hearing habeas corpus applications filed by or on behalf of aliens detained by the Department of Defense at Guantanamo Bay. The Supreme Court granted certiorari to review the decision that the petitioners were not entitled to the privilege of the writ or the protections of the Suspension Clause. The Supreme Court ruled that the Military Commissions Act (MCA) denies federal courts jurisdiction to hear pending habeas corpus actions. The Court held that pending habeas actions are subject to the statute's jurisdictional bar. The constitutional questions in this case involve whether petitioners have constitutional rights and whether Congress violated the Suspension Clause by seeking to eliminate recourse to habeas corpus. The writ of habeas corpus is important for protecting individual liberty and preserving limited government. The Suspension Clause gives the Judiciary the power to use the writ to maintain the balance of governance and safeguard liberty. The case examines whether a common-law court would have granted or refused to hear a petition for a writ of habeas corpus brought by a prisoner deemed an enemy combatant and held in a territory like Guantanamo. The geographic scope of the writ at common law is informative but not conclusive, and the analogy to British courts in India granting writs of habeas corpus to non-citizens detained in territory over which the Moghul Emperor retained formal sovereignty and control breaks down because no federal court sits at Guantanamo.

The Court ruled that detainees at Guantanamo Bay have the right to habeas corpus, and Congress must follow the Suspension Clause if they want to deny this right. The DTA and MCA were intended to limit habeas review, and the Court must assess the CSRT process to determine the necessary scope of habeas corpus review. The detainees are entitled to a prompt habeas corpus hearing, and the decision only applies to specific petitioners and does not invalidate the DTA or CSRT process. The Court of Appeals erred in determining that the Suspension Clause and its protections do not apply to the petitioners. The cases are remanded to the District Court for proceedings consistent with the Court's opinion. The author and dissenters disagree with the majority's decision to remove procedural protections for detained aliens. The DTA provides an opportunity for accused alien combatants to contest their detentions before a constitutionally adequate tribunal. The majority's evaluation of the DTA system is flawed because they did not assess the fit between the remedies and due process. The procedures provided for Guantanamo detainees are more generous than those provided for prisoners of war under Army Regulation 190-8. The DTA is an inadequate substitute for habeas corpus because detainees cannot introduce exculpatory evidence discovered after their CSRT proceedings at the appeal stage. The Court is engaging in a roving search for constitutionally problematic scenarios and inventing a reverse facial challenge, which requires no concrete showing of harm by the petitioners. The DTA can be interpreted to allow for release in appropriate circumstances.

The Court ruled that Guantanamo detainees cannot challenge their detention under the DTA as a substitute for habeas because Congress did not intend to enact such a substitute. Justice Scalia dissents and believes the Court's intervention in this military matter is entirely ultra vires. The Court's decision to extend constitutional rights to aliens held outside U.S. territory contradicts previous precedent and distorts the meaning of the Suspension Clause. The Constitution only allows for suspension of the writ in cases of rebellion or invasion within the US. The dissenting opinion agrees with the previous precedent and believes the Court's decision is flawed.