I don't know if someone has ever presented this theory, but I always seem to read about how Renegades are going to get screwed because Shepard is forced to fight Cerberus. Somehow, I doubt Bioware is willing to dissappoint and alienate a good chunk of their fans. Plus, Casey Hudson has said multiple times that no player choices will be punished.
Here is my theory when it comes to the interaction between Shepard and Cerberus:
Say in ME2, you save the Collector Base for TIM. Chances are, TIM will be grateful to Shepard for the assistance in his power-grab. So why would TIM want Shepard dead?
I personally think that for players that are Cerberus sympathizers, TIM will lose control of the main body of Cerberus, but not all of it (he may maintain the cashflow as well as a small number of troopers). The rest of Cerberus (say 75-85%) gets indoctrinated by the Reapers, thus becoming a Cerberus Break-Away group. In steps loyal Shepard. As the galactic war rages, TIM funnels resources and mission objectives to Shepard in an attempt to get Shepard to retake functional control of the bulk of Cerberus. In essence, Shepard becomes the great equalizer in a Cerberus Civil War.
This would explain why some of the new screenshots have Shepard sporting Cerberus casual wear (he still works for Cerberus and is loyal to TIM).
Perhaps it was the Cerberus troopers that were sent to the Collector Base that will become indoctrinated in the first place. The Base itself fought back...
For Paragons that decided to blow up the base and stick it to TIM, I theorize that ALL of Cerberus (including TIM) will be indoctrinated when the Reapers sweep through the (as of yet unknown) Cerberus controlled system. In this case, Paragons would finally be given the chance to plug TIM between his biotic eyes.
I can see this becoming a viable reality since Bioware doesn't need to keep the story simplified for another sequel...
Thoughts?





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