The Computer runs everything within Alpha Complex. The Computer sees everything within Alpha Complex (well, that's what It would have you believe). Everybody within Alpha Complex works for The Computer, listens to The Computer, serves The Computer, protects The Computer and quite often dies for The Computer. (it's sometimes said they often die because of The Computer, but to say such a thing is treasonous. So it's not said very often.)
Though deranged, The Computer believes it is doing the right thing. It strongly believes that Alpha Complex is in danger of being invaded by Communists (very very bad, that) or Mutants (or even mutant commies), and to this end it invented Troubleshooters, and later also Hackers. Hackers complained they weren't invented by The Computer, but those voices died out pretty fast.