User blog comment:LDR/Cerberus gone mad?/@comment-3566082-20110503174043

I have two theories:

The first theory isn't really specific but the Illusive Man might want Shepard dead for the same reason Harbinger has so much interest in having Shepard's.

It could also be that the Monolith that affected the Illusive man years ago turned him into a sleeper agent or something. At the end of mass Effect 2 Harbinger does say that the Reapers will "find another way" after the Collectors are destroyed, maybe the Illusive Man is the other way. The Monolith gave the Illusive Man the ability to understand alien languages, maybe it did this so he could collect information on the various organic races more easily.

Not sure really, all just half-thoughts of mine.