User blog comment:Mernimbler/ME3 Wishlist (Update 1)/@comment-1900300-20110411160431/@comment-184.97.47.12-20110412235354

That's something we'll find out in ME3...

My theory is that Shepard may be suffering some effects of indoctrination, and the Illusive man sees a Shepard that works for the reapers as a huge threat.

After all, he was inside a reaper, near Object Rho, and underneath Sovereign, all for long periods of time