There was also the Sega Genesis X-Men game. The whole game is supposed to take place in a hacked Danger Room, at one point you need to reset the computer and you do it by resetting the actual Genesis itself. The cartridge had to have a special battery to do this and it blew my mind as a child.
Don't forget Spec Ops: The Line, which plays on the idea of not having a choice in committing war crimes and justifying terrible amounts of violence, because you won't close the game.