You did chapter 3 wrong.Not sure I agree with the OP's assessment considering...
Chapter 1: You're run around at the whim of somebody who can only be described as a pyscopath. Otherwise, Keeper chews you out.
Chapter 2: You're basically mind controlled into doing what the SIS say.
Chapter 3: Oh golly, you got screwed over again by the Conspirators. Best you- Oh sorry, you're the Sith's bitch again.
Trooper has a lot of "Sir, yes, sir!" but that kind of comes with the military territory. Agent felt more like Cipher Nine getting dragged along for the ride by a bunch of incompetent and/or insane individuals and left to clean up the mess whilst hoping nobody would notice.
I became a republic spy