You don't have to play the good guys for the system to work, the same system is used for Dune - Adventures in the Imperium, and that's a setting about as morally grey as it gets. Even with Star Trek Adventures, there is the Klingon Core Rulebook if you want to be a bit more rowdy than your typical Starfleet officers. The Operations Division sourcebook has suggestions for playing as Section 31 as well.