CptSketch13 wrote...
true cerberus did start as an alliance black op
Yes, in fact the first game, and even the second, did an interesting job of portraying shades of gray.
Consider the missions you get sent on in ME1. The best example is UNC The Negotiation (which you only get as renegade). You are supposed to go talk to "Lord" Darius at the request of Hackett, although he sends you knowing full well that there is likely to be a fight and Shepard will probably end up killing Darius. Very ends justify the means sort of deal.
And there is the UNC Dead Scientists mission, which anyone can get. Cerberus set up the thresher maw attack on Akuze, and was experimenting on Cpl Toombs. When Hackett sends you on the mission he says that several Alliance scientists have turned up dead... You could potentially interpret that to mean that the whole thing was an Alliance operation when Cerberus was still a part of it. Of course you could also simply believe that those scientists were clandestine agents of Cerberus even though they were in the Alliance, so Hackett didn't know they were part of Cerberus.
That's really the only semi-anti-Cerberus mission that Hackett sends you on. UNC Cerberus and UNC Hades' Dog come from Kahoku essentially. Other Cerberus related missions you stumble on by chance (The Listening Post Alpha and Theta missions and Depot Sigma-23).