Title says it all, if he / she wasn't the one who blew up the mass relays why is he even on Earth in the first place? Also how come if you side with Cerberus and save the collector base they turn on you. If the Illusive Man's reasoning for wanting you dead is that you are causing him trouble its a huge contradiction that if you side with him he still feels this way.
Did I miss something? If so feel free to point it out.