The decision in this case is usually hailed as a landmark for liberty, but while the decision is correct, there are some problems with the opinion that leaves open the door to abuses that have recently become topical.
The main problem is that it seems to accept the authority of military tribunals to try persons is a state of actual war or in an area where "the courts are closed". It is one thing to detain persons until civilian courts can try a case, and quite another to try and punish them. It is also a problem when the courts are closed as the result of action by the military forces that detain and try, and it is also a problem when there is not an actual declaration of war (since letters of marque and reprisal only apply to expeditions outside national territory), even if the situation might be described as an "insurrection". It might be argued that indefinite detention might be authorized in the situation that Congress is unable to meet to declare war, but that was not the situation in this case, even if withdrawal of some of the states raised a question of existence of a quorum. It also seems to accept that the U.S. Congress might have the authority to enact criminal penalties against individuals engaged in rebellion, when the Constitution confers no such authority outside territories ceded to the exclusive jurisdiction of a state under Art. I Sec. 8 Cl. 17 or territories under Art. IV Sec. 3 Cl. 2. The lack of provisions for doing all of these things may be considered a defect in the U.S. Constitution that might require amendments, but unless or until such amendments are adoped, the authority does not exist. The only constitutional way to detain and punish persons in any such situation is under state statutes and in state courts.
The opinion neglects to emphasize the important principle that jurisdiction in all matters of criminal law is primarily territorial, not personal, except for military personnel or militia personnel in actual federal service, in accordance with Art. I Sec. 8 Cl. 14 and 16. This means there is no criminal authority for acts committed outside U.S. territory, except for military personnel (since militia personnel may not be used outside U.S. territory), regardless of where the effects of the acts might occur. The word in the Constitution is "committed" not "occurred", Art. III Sec. 2 Cl. 3, which means the location of a crime is that of the offender at the moment actus reus is united with mens rea.[1]
[1] Introduction to Conflict of Criminal Laws, Edward S. Stimson (1936).