In this case, the mutant wasn't just captured in the U.S. He's also a U.S. citizen.
The only terrorists who could be subject to something other than U.S. criminal prosecution (assuming they are captured alive) are foreign nationals captured outside the jurisdiction of the U.S.
The mechanism is called war powers. If a US citizen fights against the US or is a traitor then they can bull doze the for all I care. You forfeit your tights when you attack the country.