Okay here is another theory I came up with, or just an old theory coming back to disccusion.
As I said before/ posted on here Ceberus has been slowly following the Reapers agenda ever since ME1, and maybe for ME1.
TIM started Cerberus after he was touched by the Monolith on Shanxi. He heard Voices when ever he was asleep, or knocked out, and saw visions of planets, and other things that seemed like a warning beacon in a sense.
Anyways TIM started Cerberus, but Cerberus was not protecting humanity, the way everyone thought of. Instead they attacked political, economic,military, and reaserch centers that were non human, weakening the galaxy, and causeing bad relations for humanity for the galaxy.
Cerberus was experimenting on humans their own kind. We learn from Toombs that Cerberus used his squad as test subjects, and he managed to survive, but had Thresermaw venom in is body. Admiral Kohakoo was trying to find his squad, but when we report back to him, that his squad is KIA, he goes on a hunt/ Vendetta to find the people that set a trap that killed his team.
Later on we find out that Cerberus was behind the Admirals squad's deaths. As we take down Cerberus bases, Admiral Kahokoo found the main Cerberus base that is houseing the Reaserch. After seeing Thrall Thorian huks, Rachni, and Husk, we find The Admiral dead.
There is more on what Cerberus did in ME1, but let's go onto ME2. TIM want's Shepard on his side, heck anyone would. Shepard has become the vision of humanity, and what it should be. If you notice if you go Renegade/ let the Councile die. You did what Cerberus has always wanted. Heck TIM even says that Shepard killing the councile has helped humanity dominate the galaxy.
Ya thanks Shepard.
Anyways I wish I could add more, but my phone is about to die.
I will say this before I go.
Renegade Shepard in ME1, and ME2 follows Cerberus goals, while Paragon Shepard follows the counciles goals/ the Alliance goals.
In ME3, Renegade Shepard is in line with Cerberus goals helping humanity at all cost. Yet Paragon Shepard is falling into Cerberus goals hence Shepard as a Paragon starts to wonder " What if the illusive man is right, and he can control the Reapers?"