Chignon wrote...
I never heard of this theory. I'm curious.
Where does Cerberus going rogue or not from the Alliance play into the Alliance also doing something to investigate and protect the colonists? I mean, I can see why if Cerberus didn't go rogue. But if it didn't?
A political and military contruct as influential and powerful as the Alliance won't always stick to the rules, in my opinion. But this doesn't necessarily mean that Cerberus is still a part of them and is financed by them.
Kahoku claims they've gone rogue from the Alliance in ME1. But he's the only evidence you get for that assertion. Not to disparage the deceased, but the man was killed and in a way that makes absolutely no sense to me unless Cerberus was a) a bunch of psychopaths (certainly possible)

covering up its Alliance connection. I'll have to replay the missions with Rachel Shepard to be absolutely certain there is no other evidence, but I really don't remember any.
Miranda says Cerberus is, "privately funded." The Alliance could very well be one of those private investors.
Anderson is entirely non-plussed by your sudden appearance from the dead, his email is also waiting for you when you get your ship. The human coucilor is a powerful individual, but
no one , not even Udina, reacts to your resurrection appropriately.
No one registers surprise. (I'm not going to touch Tali & Garrus & the VS's lack thereof in this post.) And all he does is go silent on Kaidan's activities. He doesn't arrest you, certainly within his power, his belief in the Reapers not-with-standing. He doesn't give you another out, which when you regain your Spectre status, is certainly within his purview as well, he just pats you on your head and sends you on your way.
Then... the most telling part. TIM claims that he can't tell you where Kaidan is because his file has been rendered "blacker than black ops," if I'm remembering the quote correctly. Yet, TIM finds out about his presence on Horizon quickly enough to arrange the little demonstration for Shepard. While it's certainly possible TIM is lying about not knowing anything about Kaidan's whereabouts, the fact that he even knows that Kaidan's got that kind of security around his file is in an indication of very high-up contacts, or collusion within the Alliance itself.
Finally: it's
Martin Sheen. They're not going to waste that kind of coin on a VA without something major planned, and being a Bond villain is certainly below Sheen's talents.
It's all circumstantial evidence... but that's all we have: conjecture and supposition. From what I've heard about the books (which I should really get one of these days), there's even more small clues to the connection.