I agree on that as it were we're still with the Alliance just one of their black ops projects. That they say went rouge in reality their still operating within the Alliance. Kind of like Al Qaeda, with the CIA.
Nothing actually shows that.
Pre-ME1 - Black ops, with much infiltration of humanity
ME1 - Black ops but going rogue, with some infiltration of humanity
ME2 - Broken off and declared terrorists, with less infiltration of humanity now that they're more in the open
ME3 - Broken off and a direct threat to humanity, and any sympathizers are to be stopped
Again, nothing shows that they're part of the Alliance anymore. Even if Hackett was okay with them before (and a bit of ME1-ME2 might indicate that he at least understands where they're coming from), by ME3 they have crossed any moral event horizon and even if there were some in the Alliance that supported Cerberus, they would be considered total traitors by even the other higher ups.
EDIT: However, this is largely due to TIM's leadership of Cerberus. The Alliance itself likely has many individuals in it that support off-the-record research and development, even if it strains or breaks ethics. TIM took the organization one way, while the Alliance went the other way, when they once worked more hand-in-hand.





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