Paranoia has Troubleshooter characters who a nominally good guys, but they spend most of their time backstabbing each other for obsequious favour ti a tyrannical and autocratic Computer. They are essentially playing a SS group of enforcers for a totalitarian state, if you think too hard.
I think I could also make an argument for Delta Green. This is a game where it's completely reasonable for Investigators to frame an innocent man for murder if it means accomplishing their mission. It's one of the few campaigns where I had a PC send a kill squad after an innocent family to recover an alien artifact from the teenage son who didn't know what he had.The only game I know where the character is a villain is Vampire: The Masquerade.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.