Long story short, the court not only didn't buy Yoo's claim of immunity but stuck it up his sorry ass by citing Alexander Hamilton in the Federalist Papers:
Lest we forget, Padilla is an American citizen who was arrested with great fanfare in May 2002 for being a player in a plot to make a "dirty bomb" and detonate it in a major U.S. city.
[War] will compel nations the most attached to liberty to resort for repose and security to institutions which have a tendency to destroy their civil and political rights. To be more safe, they at length become willing to run the risk of being less free.
Those charges eventually evaporated, but Padilla continued to be considered an "enemy combatant" and was tortured at the Navy brig in Charlestown, South Carolina. He eventually was convicted of lesser charges in a civilian court and is serving a 17-year sentence.