Some of what was lost is now regained ...
There are spoilers after the break. Continue reading at your own risk.
Meriel's Personal Log, Entry Three
Location: The Cerberus Facility/ The Normandy 2.0
Credit must be given where credit is due. The Illusive Man is a master of manipulation. This should not come as a surprise given the man's position, and indeed it does not, but he certainly takes a different approach than most. Most individuals seeking to gain control of a situation would seek to manipulate from behind the scenes in a manner that remained undetected by the individual being manipulated ... until it was too late. The Illusive Man, on the other hand, lays it out on the line. He knows that I should feel indebted to him, after all he resurrected me (so to speak). He could hold that over my head, but instead he chooses not to. Instead he openly seeks to bind me to Cerberus with pending doom, "limitless" resources, and frank appreciation for the achievement of desired results. For instance, after returning from Freedom's Progress he had no harsh word regarding my defiance of Miranda's wishes. Instead he praised my methods, acknowledged that they were different than his, and said that he could not argue with results. That is something that the Council never would have done, and he damn well knows it. He knows he's playing me, he knows that I know he's playing me, but he knows that he can get away with it because he has information and resources I need. He knows that no one else has both the resources and the willingness (read: disregard for proper protocol and diplomatic channels) to track the Collectors and the Reapers. That is one very powerful trump card. There is also something else he has that no one else does.
No one else has Joker.
Joker. Friend. Confidant. The man I lost my life saving. Those are some very strong, very powerful emotional ties - especially for someone who for too long trusted no one but herself. The Illusive Man offered up Joker (and with him a redesigned Normandy) as an extension of his good will. Good will or not, the Illusive Man knows that I have been drowning in this sea of unfamiliarity. By giving me back the Normandy, by giving me back Joker ... words cannot express what they means to me. He knows this too. The Normandy was the first place that I really felt I belonged. Not only that, but she is a symbol of power, a symbol of defiance, a symbol of humanity's triumph. Then Joker. Where do I begin? Joker always knows more than he lets on. I trust him implicitly and, outside of Garrus, there is no one else I missed more after my revival. Garrus always had my back from a firepower standpoint, and Joker always had my back in everything else. He's just a little insane, and that means he is willing to take necessary risks that others would advise against.
It was nice to see Tali on Freedom's Progress, but she and I used to share more of a mentor/mentee relationship. She is commanding her own soldiers now. She does not need me. Also, as the Illusive Man so expertly pointed out, two years is a long time. Most of my old team has moved on or, according to him, changed their allegience. Garrus went missing not long after I was declared dead. Ashley is deep within the Alliance and unreachable. Wrex is tied up trying to re-unite the krogans, and Liara is likely working for the Shadow Broker, of all people. Everything he told me, knowing how it would make me feel, simply reinforced the emptiness I've been carrying inside. The presence of Joker has helped fill that hole a little bit. With Joker tied to The Normandy 2.0, and me tied to Joker, the Illusive Man as in effect tied my body (even if he has not tied my mind) to Cerberus. He knows that of all the people in the world, I would never abandon Joker, even if my life depended on it. After all I have already risked, and achieved, death for the man. Why would I not be willing to do the same again?
Perhaps sensing my distrust of Miranda (something I have made no secret of ), or perhaps simply having new things for her to do, the Illusive Man also managed to recruit Dr. Chakwas to be part of my medical crew. Two years ago, from an emergency pod, she said that she "watched the Normandy crumble with [me] on board." That must have been a horrifying sight. After that she found a position planet side, but claims that it simply was not the same as working aboard a starship. While Chakwas understandably has little trust for Cerberus, she said that she joined their cause because of me. She believes that all my dealings with this organization will be ethical. She trusts me. Dr. Chakwas, a woman who has been with the navy for years, left the Alliance for this post because ... she trusts me. What did I ever do to earn that kind of loyalty?