User blog comment:SilencedSkies/The Illusive Man: Good, Evil or just bad writing?/@comment-1900300-20120412065117/@comment-5017885-20120414051436

To be perfectly fair, the Reapers never do have an actual alliance with the Illusive Man. They simply manipulate him, and by extension the Cerberus organization itself, into accomplishing their own goals. In manipulating Cerberus into fighting with the Alliance, the Reapers essentially forced a Human Civil War, weakening humanity as a whole.

In fact, from what is presented in-game, it can be concluded that dividing and conquering is standard Reaper strategy. Javik himself relates that the Reapers did much the same in their war against the Prothean Empire, manipulating the Protheans into fighting each other over whether to destroy or control the Reapers: exactly the same clash of ideas presented in the conflict between the Alliance and Cerberus.

Cerberus troops, while indoctrinated and implanted with Reaper technology, are under the sole control of the Illusive Man via the technology developed on Sanctuary; there is never an instance, really, that Cerberus troops and Reaper troops are seen aiding each other. In every instance they're in the same area, they fight each other.

As for the Illusive Man, he hasn't really changed his stance. There was always a sense that he had a nefarious ulterior motive since his introduction in ME2, and it's in fact hinted at in the ending decision: whether to destroy the Collector base (with all of it's Reaper technology) or to give it to Cerberus (so the Illusive Man can try to learn how to control it).

I won't go into the ending, however, as I'm an avowed supporter of the Indoctrination Theory. The endings taken literally are simply too stupid and cliche to be taken seriously.