Cerberus have been somewhat inconsistently portrayed throughout the trilogy.
In ME1 they were a largely unknown Alliance Black Ops outfit gone rogue.
In ME2 they were a human supremacist terrorist group known to any number of factions and individuals.
In ME3 they were the Evil Empire. An army able to operate across space and the second greatest threat to galactic civilisation.
Cerberus appears to be a radically different organisation in each instalment of the trilogy. In ME2 they were clearly retconned , while the ME3 incarnation existed largely to provide an alternative enemy faction (their role in the game having more to do with the requirements of multiplayer than the actual story).
It would be easy to dismiss all this as laziness on the part of the writers but I think these changes can easily be accommodated within the lore. This actually requires very little head cannon, as long as the following questions are addressed.
1 : How can ME2 Cerberus be the same organisation from ME1?
2 : Why is the existence of Cerberus common knowledge in ME2 while it was almost completely unknown in ME1?
3 : How does Cerberus transform itself from the small if powerful organisation Shepard worked with in ME2 into the
massive military machine he/she fought against in ME3?
Question 1 : How can this be the same organisation?
Cerberus are known to have agents and supporters within the Alliance military. This is assumed by most people in ME2 while the large presence of ex Alliance personnel within Cerberus and the group's involvement in the design of the original Normandy confirms this. I think that the group encountered in ME1 are a Cerberus cell working undercover as an Alliance Black Ops outfit.
There is an in game precedent for this kind of covert action by Cerberus. In ME2 during Jack's loyalty mission on Pragia one of the Cerberus scientists talks about shutting down the Teltin facility and instead piggybacking onto the Alliance Ascension program.
What Rear Admiral Kahoku discovers in ME1 is a similar infiltration. Without prior knowledge of Cerberus, Kahoku assumes the organisation to be an Alliance project rather than part of an outside agency (an understandable error as it's actually both) . Kahoku's investigation is blocked by Cerberus agents and supporters within the upper echelons of the Alliance.
The Cerberus of ME1 is a single cell, one part of the organisation embedded within the Alliance. The Cerberus of ME2 is the greater part of that organisation.
Question 2 : Why is Cerberus so well known in ME2?
Two years is a long time in politics. I think that Kahoku's investigation and subsequent murder in ME1 reveals the existence of Cerberus to a wider galaxy. The assassination of such a high ranking Alliance officer becomes a major scandal that Cerberus is unable to contain. Further investigation of Cerberus brings to light numerous operations going back years. Only after the events of ME1 is the long history of Cerberus discovered. Numerous terrorist acts and controversies previously thought unconnected are now attributed to Cerberus. As a result Cerberus' influence within the Alliance is substantially reduced by ME2. By the time Shepard is revived in ME2 Cerberus are infamous throughout the galaxy.
There are real life examples of this situation. The Watergate Affair in 1975 prompted a much wider investigation into illegal and morally dubious actions by US intelligence agencies. While Watergate itself was an act of petty burglary the resulting scandal led to the Church Committee hearings the same year. The Committee discovered that Watergate was positively moribund in comparison with other governmental crimes. Senator Church revealed a catalogue of crimes committed by the CIA, FBI and NSA most of which had been kept from the public for decades. A more recent analogy would be Al Quaida , who were active for several years before becoming a household name with the attack on the USS Cole in 2000.
Question 3 : How did Cerberus become an army in ME3?
The Illusive Man is aware of the Reaper threat and has prepared accordingly. There is a reference to military mobilisation in the Cerberus entry in ME2's Codex :
'Counterterror experts speculate Cerberus may have changed leadership with it's recent shift to STOCKPILING SHIPS, AGENTS AND WEAPONS' ( Emphasis added )
The change in leadership is pure speculation as the Codex entry makes clear but the reason for the shift in policy is undoubtedly the events of ME1. Sovereign's attack on the Citadel is final proof of the Reaper threat while the destruction of the Alliance cell and subsequent loss of influence within the human military makes Cerberus humanity's first and last line of defence as far as the Illusive Man is concerned. Cerberus know that war is coming and now need their own army.
While Cerberus have been building the infrastructure for an army since before ME2 their successful recruitment drive in ME3 is explained in game. The Sanctuary facility is used to convert civilians into shock troops using Reaper tech and indoctrination .Cerberus has been researching this as early as ME1. Sanctuary only starts operating once the Reaper invasion is underway but all this has clearly been prepared for in advance. This scheme may well have been set in motion as soon as Shepard was sent to Horizon in ME2.
The Cerberus troops encountered on Mars have been recruited and augmented from regular Cerberus personnel prior to the Reaper invasion. It is quite feasible that these early ME3 Cerberus encounters are with a limited strike force and don't necessarily suggest Cerberus has an entire army quite yet. Cerberus has a military wing but only has an army when Sanctuary is up and running. This is possibly why General Petrovsky has to supplement his own forces with Rampart Mechs and use Containment Fields to police Omega. He simply doesn't have enough troops at this point.
None of this contradicts the nature of the organisation in ME2. Cerberus are certainly larger than previously thought but only become an army after the Reapers invade and Sanctuary starts up. In ME2 our main sources of information regarding Cerberus' size and organisational structure are EDI and Miranda. I doubt either lied to Shepard but they simply wouldn't have access to all Cerberus data . Compartmentalisation is standard MO for this organisation.
In the Omega DLC General Petrovsky is described by Aria as the Illusive Man's best kept secret. Given this and his military rank I think Petrovsky was tasked with building up Cerberus' nascent army from ME1 onwards. This became a priority when the Illusive Man lost his influence in the Alliance military as outlined under Question 2. The mobilisation was in anticipation of the Reaper invasion and was kept separate from all other Cerberus operations until then under General Oleg.





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