Maybe you preserved the Reaper facility, but if you blew it sky high and thought that the Reaper's secrets were lost to the Illusive Man forever... Well, think again. Whether you chose the Renegade or Paragon option in the final mission of Mass Effect 2
, the Illusive Man recovers information about the experiments the Reapers performed on the colonists and he has an epiphany that could rival Anakin's thought process when he tries to strangle Padme in Episode III
: I just spent trillions of credits bringing Shepard back to life and assembling a team to stop the Collectors from abducting more human colonists for Reaper experiments. Now that she has done the impossible, I think I will just continue those experiments. (Yeah, Illusive Man, no way you are indoctrinated. This all makes perfect, logical sense. I'm sorry for doubting you. I'll go back and make that Renegade choice now.) For the greater good of the human race, of course... Oh, and revenge.
In the novel, Mass Effect: Ascension, we are introduced to Cerberus operative Paul Grayson. The Illusive Man entrusts Grayson with one of his investments, a girl with enormous biotic potential, named Gillian. Eventually, though, he turns his back on the Illusive Man to keep his daughter and Kahlee Sanders safe.
The Illusive Man does not just get even with those who cross him. No, he is more of a I am going to conduct experiments on you with alien technology, turn you into an abomination, take notes on it, and then kill you kind of guy. While implanting Grayson with Reaper technology, the Illusive Man calmly explains that these nanides will eventually spread through Grayson's entire body, turning him into an organic host for the Reapers. He's like a Bond villain, except he actually carries out his evil plan while explaining it.
Through Grayson, we see the brutal process of indoctrination. In the beginning, Grayson still has control of his body while the Reapers sleep. But even in the early stages of indoctrination, the Reapers have latched onto his thoughts, making him believe they are his own. Grayson contemplates ending his life, but after losing a vessel once before to suicide (Saren), they are able to manipulate him into thinking he has decided that would be cowardly. Grayson also physically changes, beginning to look more machine than man.
The Reapers eventually gain complete control of Grayson's body, using him to gather information about the Alliance school for biotic children. Cerberus acquired data on this final stage of indoctrination, as well, through a man called Kai Leng.
Cerberus continued to study indoctrination and the basis of Reaper technology, as seen in Mass Effect: Invasion from Dark Horse Comics.