The U.S. government argued:
A non-resident enemy alien has no access to U.S. courts in wartime.
These non-resident enemy aliens, captured and imprisoned abroad, have no right to a writ of habeas corpus in a court of the United States. (See Ex parte Quirin)
The Constitution does not confer a right of personal security or immunity from military trial and punishment upon an alien enemy engaged in the hostile service of a government at war with the United States (In this section, the Army quoted the Geneva Conventions, implicitly recognizing that the prisoners had rights and obligations under them.).
Decision
In their ruling, the Supreme Court justices noted (emphasis added and footnotes removed):
…Modern American law has come a long way since the time when outbreak of war made every enemy national an outlaw, subject to both public and private slaughter, cruelty and plunder. But even by the most magnanimous view, our law does not abolish inherent distinctions recognized throughout the civilized world between citizens and aliens, nor between aliens of friendly and of enemy allegiance, nor between resident enemy aliens who have submitted themselves to our laws and non-resident enemy aliens who at all times have remained with, and adhered to, enemy governments. …
But, in extending constitutional protections beyond the citizenry, the Court has been at pains to point out that it was the alien's presence within its territorial jurisdiction that gave the Judiciary power to act. …
If this [Fifth] Amendment invests enemy aliens in unlawful hostile action against us with immunity from military trial, it puts them in a more protected position than our own soldiers.
We hold that the Constitution does not confer a right of personal security or an immunity from military trial and punishment upon an alien enemy engaged in the hostile service of a government at war with the United States.
…It is not for us to say whether these prisoners were or were not guilty of a war crime, or whether if we were to retry the case we would agree to the findings of fact or the application of the laws of war made by the Military Commission. The petition shows that these prisoners were formally accused of violating the laws of war and fully informed of particulars of these charges.