Mahoney v. United States was a Supreme Court case that dealt with the issue of whether a federal court had the power to issue a writ of habeas corpus to a prisoner held in military custody. The case arose when a prisoner, John Mahoney, was arrested by the military and held in military custody without a trial. Mahoney sought a writ of habeas corpus from the federal court, which would have allowed him to challenge his detention. The government argued that the federal court did not have the power to issue such a writ, as the military was not subject to the jurisdiction of the federal court. The Supreme Court ultimately ruled in favor of Mahoney, holding that the federal court did have the power to issue a writ of habeas corpus to a prisoner held in military custody. The Court reasoned that the writ of habeas corpus was a fundamental right that could not be denied to any person, regardless of their status. The Court also noted that the writ of habeas corpus was a necessary check on the power of the military, and that it was essential to ensure that the military did not abuse its power. As such, the Court held that the federal court had the power to issue a writ of habeas corpus to a prisoner held in military custody.

In the case of Mahoney v. United States, the Supreme Court was asked to decide whether a federal statute that allowed for criminal prosecution in cases where an individual had been previously pardoned by the President was constitutional. The majority opinion held that it was, but Justice Field dissented on two grounds: firstly, he argued that such a law violated due process as guaranteed by the Fifth Amendment; and secondly, he contended that Congress did not have authority under Article II of the Constitution to pass such legislation. He reasoned that since only Congress has power to grant pardons or reprieves for offenses against its laws (Article II), then any attempt by Congress to limit or modify those powers would be unconstitutional. Furthermore, he argued that allowing criminal prosecutions after presidential pardon would violate due process because individuals should be able to rely on their pardon as protection from further punishment once they have received it from competent authority - namely, in this case being granted by executive order from the President himself.