So, here's one of my headcanons about the Alliance in
#MassEffect being abso-fucking-lutely not as squeaky clean as a lot of people think. You keep getting hints that Cerberus "was" an Alliance Black Ops. We don't get an all too clear picture how long, exactly that went, although I'd say that Cerberus definitely has unilaterally cut ties before attacking the Mars archives in ME3.
The whole time Shepard basically gets to roam free even around the Citadel after flying in on a ship sporting Cerberus colors, and possibly a big, fat Cerberus logo on their armor? The Council screams "terrorists", but will leave you unchallenged? Even the Chief of Security is unbothered, regardless of whether you take the empty Spectre title or tell the Council to stick it? You just have to get an impression that one is an official position, while the actual position throughout ME2 is quietly condoning your actions. Up to and including blowing up the Bahak system.
Speaking of which, Hackett puts this mission to you. Fleet Admiral Hackett of the Alliance comissions a black op of Shepard, in Cerberus employ, going to Bahak and "bust out my good friend". He supposedly knew nothing about the Reaper artifact, the Project, and blowing up the relay? Yeah, pull the other one, it's got bells on. Going down certain dialogue options with Hackett after the mission, he outright tells Shepard that they'll be a handy scapegoat for the outrage.
I think the truth as planned was more like the story of Banes in ME1 - Shepard was supposed to suffer a staged, "fatal accident", and go to Cerberus that way. Only the Collectors made the accident real, and a race for Shepard's body ensued. In which the Alliance was, again, curiously idle. So I come to conclude, while the Alliance may officially condemn Cerberus, for a much longer time than we are led to believe, Cerberus is the dirty job arm of the Alliance. The deception works the other way, as well - by painting the Alliance as idle, complacent, and subservient to the Council, the human potential is brought to bear on both fronts, cooperating at the surface, and playing dirty under the table - in secret, both in the same, coordinated interest.
While the Citadel DLC is mostly fanservice and in-jokes, there is something unnerving about the identity theft quest with Shepard's clone: Why was the clone abandoned by Cerberus? Was it really because the Illusive Man wanted the "real" Shepard? Or was it because the clone proved unstable and uncontrollable for some reason? Maybe that reason is Shepard being as much a product of genetic engineering as Miranda. The backgrounds do not exclude that - as a spacer, with all the implicated rules about fraternization, how is Shepard exactly the kid of two serving officers? As a colony kid, how do they survive the Batarian attack as a teen? And a street kid gets to excel how in the military? The Starchild says something remarkable: "You changed the variables". Is it a fluke of nature, or much more the result of not quite stable, not quite legal, genetic tampering? Which would also explain why Shepard was of such interest to the Collectors and the Reapers. The real danger was never the fighting spirit, the ability to inspire, although that would get them to the goal - the danger was the transformative result of something built into their genes.
So what I want to say is... the mechanic on Horizon in ME2 might not be the conspiracy nut that he appears to be. He might not be all that wrong about the Alliance feeding propaganda to its citizens, Shepard themself cleans up a fair share of messes in ME1, gets framed in the Arrival DLC of ME2, and seemingly got detained without trial or process inbetween ME2 and ME3. The events surrounding Saren and Sovereign are played down, hushed up, and Shepard practically thrown down a memory hole. So... be careful of grandpa Hackett. He's up to no good, and may only look like the better alternative when put up against the Illusive Man.
