The next day, Shepard went to consult with EDI, the ships AI. EDI was originally a Cerberus machine, but like Shepard and Maranda, broke away. Heck EDI did it twice, hyjacking a Cerberus inflitration bot to use as a body. Said body was off the ship, on earth with Joker, helping him get rest. But EDI was still on the ship too, able to split her mind quite effectively. Course even then, she still couldn't help.
"What the hell do you mean, you can't?"
"I'm sorry Shepard, although I can locate the chip in question, I do not have the ability to interface with it. This chip's only ability to communicate, has been deactivated. It was likely the part that was awaiting signal for the Illusive Man's death, now that he is dead, that part has been disabled, thus no way to remotely get to it." EDI explained calmly, the little holographic ball that was her original avatar showing before Shepard.
"Can't it be turned back on?"
"Internal functions or direct interface would be required. I do not see a way of directly interfacing with the chip while keeping you alive."
Shepard sighed, glaring over to wherever the Illusive Man showed himself, figuring he would be there to gloat. "How about it, care to turn your little transmitter and receiver back on? Maybe the real you is alive and trying to tell you to stop?"