Dean MacArthur and the follow-up contact Leonard give one of my favorite combined arcs for being a villain in charge.
I also like Brother Hammond's arc (15-24 Cap au Diable) for the same reason. The player character is the instigator and not a stooge.
Barracuda Strike Force. After you unwisely free Reichsman, "you don't remember exactly what happened", but everyone wakes up in a separate 5th Column jail cell.