Alpha Complex is an enclosed, underground city, isolated from the devastation of the outside world, and tyrannically ruled by a dysfunctional and delusional Computer. The Computer isn't thoroughly aware of the world outside of Alpha Complex, and regards it with fear and suspicion, while it governs the Complex itself with edicts sourced from it's vast data store of old, often confused, and commonly contradictory data files. The Computer attempts to defend Alpha Complex from it's percieved enemies - Communists, Mutants, and Traitors.
The players take on the roles of members of a team Troubleshooters - Newly-promoted citizens of Alpha Complex, whose role is to seek out trouble, and shoot it. This includes seeking out Enemies of the Computer, and terminating or capturing them, for the glory of Alpha Complex, and Friend Computer!
The one small flaw in this brilliant plan? Every citizen of Alpha Complex is either a Communist, a Mutant, or a Traitor, in one fashion or another. Every player has a mutant power, and belongs to a traiterous secret society. Add in confused, misleading, or completely incorrect assignments, badly labeled and often dangerously experimental equipment, and many players with often competing goals, and it becomes obvious why Troubleshooter missions are so often fatal.
Essentially - You will be given a mission, which may not even be possible, you will be given equipment, which may kill you just as certainly as your opponents, you will be part of a team of commie mutant traitors, who will most certainly be trying to kill you first, you will be given additional personal goals, which may be mutually exclusive with your mission or leave you directly competing against your teammates, and you have to deal with all of this in a dystopian nightmare city, goverened by an eccentric, senile, confused Computer, who holds ultimate authority over the entire complex, and will order your termination on a whim.