Justice Thomas wrote a 15-page dissent from the denial of certiorari that was joined by Justice Scalia. Justice Thomas argued that the issues raised in General Noriega's case should be considered now because they apply to a large number of persons being detained by the United States. General Noriega's petition "presents an opportunity to decide the constitutionality…of federal statutes…in time to guide courts and the political branches in resolving difficult questions concerning the "proper exercise of governmental power…and…spare detainees and the Government years of unnecessary litigation.

General Noriega's case addresses an issue left undecided by the Court, which is whether Section 5 so narrows the scope of habeas review under 28 U.S.C. §2241 that it "effectively works a suspension of the writ." Review would also likely settle such questions as whether the Geneva Conventions are self-executing and whether the federal courts may classify detainees as POWs, as United States District Court Judge William Hoeveler did for General Noriega. As Justice Thomas observed, "addressing these questions now…would avoid years of litigation and uncertainty no matter what we conclude on the merits." At this juncture, General Noriega only needs two more Justices to agree that it is in the national interest to reach these issues now."