Bad King wrote...
I doubt Kahoku got it wrong- his info was mostly bought from the Shadow Broker who has a reputation for providing top quality info. Besides that there are other clues in the game- Dr. Wayne, one of the scientists responsible for Akuze was an Alliance scientist (confirmed by Hackett)- of course Akuze occurred before the split, so it was an Alliance project. As for the codex getting it wrong, that makes perfect sense- the primary codex tends to reveal information only known to the public (there's a lot of false info regarding the protheans and reapers etc). The Alliance have been working hard to cover up their ties to Cerberus- if the public discovered that Cerberus was once part of the Alliance, it would be a scandal, and there would certainly be a backlash against the Alliance. So better to claim that Cerberus has always been an independent terrorist organisation than a secret department of the Alliance that went rogue.
Now for a bit of speculation!
My theory is that there is no retcon and that after TIM founded Cerberus, he merged the small organisation with the Alliance. Under the Alliance the group grew, and by ME1, TIM decided to split with the Alliance in order to give Cerberus more independence- this would allow them to be regulated less by the Alliance which in turn would allow them to make better preperations against the Collectors/Reapers due to increased freedom. With their newly gained freedom hey started the super soldier projects to create shocktroopers (Thorian Creepers and Rachni) to aid humanity in the coming conflict with the reapers. The chief operative in charge of this was Armistan Banes who faked his own death to escape the Alliance and blackmailed Dr. Chloe Michel for supplies for the project. When Kahoku investigated, Banes made sure that a fake body was left. However Banes was afraid that the conspiracy would still be revealed by Kahoku's marines and so lured them into a Thresher maw nest, and later killed Kahoku in order to cover up the projects.
Ah yes, Dr. Wayne. I had totally forgotten about him. Thanks for the reminder.
I have to say though that the codex is kinda selective as to when it gives public information and when it doesn't. Example, Indoctrination has its own codex entry, but is not public knowledge. The Cerberus entry could indeed be just public information or still a retcon. We can't know for sure, because like I said, the Codex is selective.
Now about your theory. I was wondering, why would the Alliance, a public and governmental body and the face of humanity to the galaxy, agree to merge with Cerberus, a private organization?





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