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.
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.