While Rei goes out to fight the latest Angel in her EVA, Shinji is stuck at base, waiting to be given the signal to attack. But his father holds him back for now. Shinki remembers how Rei found out that she liked having Shinji touch her. It made her feel... warm, inside.
But the Angel is messing with her EVA, and it starts taking over her EVA, making strange bulging vein-type structures appear over her body. She has a vision of herself talking to her, and realizes that it is the Angel. But it is taking her over and Shinji is sent to help her. He tries to attack the Angel, but it starts taking over his own EVA, with many of the same affects. When Rei realizes what is happening, she gathers the Angel to herself and sets her suit to explode, which it does.
Shinji is devastated by what has happened and his inability to prevent Rei's death. Actually, she hasn't been declared dead yet, but he knows it is just a matter of time. Shinji spends his time with Kaworu Nagisa, a fellow schoolmate and pilot who seemingly hates Shinji, and is actually another Angel, this one in human form. Shinji cannot deal with Rei's death, nor with people who would try to comfort him, so he stays with someone who hates him instead. Kaworu kisses Shinji to prevent him from having problems with his breathing, which leads Shinji to remember Rei once again.
Shinji doesn't come home for days, until the rescue team recovers Rei from her suit, and somehow finds, amazingly, that she is still alive! Shinji is overjoyed, but when he goes to see her, there is something wrong with her. She seems to have gone back to the way she was when he first met her. It is as if it wasn't *her* at all. When he thanks her for saving him, she says she doesn't remember. Maybe because she is the third one.
Third one? What can she mean? While Shinji tells his guardian Misato about Rei's words, the Doctor of the facility, Dr. Ritsuko Akagi, remembers how her mother came to work at the facility and got her hired. That's where Ritsuko met Rei for the first time... the first one. As in the present time, she is questioned by the members of Seele, she remembers how her mother began to hate the little girl, then killed Rei and herself.
After the questioning, Misato and Shinji show up and take Ritsuko hostage, wanting to know Rei's secrets. And they are revealed. Rei is a clone, or, actually, a series of clones, made to be dummy plugs for the Evas. The EVAs were created by humans, and so was Rei, made to be the housing for her soul. Every time she dies, her soul is downloaded into another body. Ritsuko can no longer stand it, and kills the remaining bodies all at once, then breaks down as she confesses the details of why she kept doing this. Like her mother, she had fallen in love with Shinji's father, Gendo Ikari. But she was a fool, like her mother was a fool, because he doesn't love her.
As she cries, Shinji and Misato look at each other, wondering what to do next...
The anime for this series is one of the most confusing stories ever, and the manga series is better in terms of not being confusing, but not exactly being a story I enjoy. Secrets pile on secrets, and the characters all seem hampered by the secrets, wanting them to be uncovered, but the toll of those secrets is harsh when they are finally uncovered.
This is an intriguing manga, but you could die of anticipation waiting for the next one to come out, so I can't exactly recommend it. If you like your giant mecha series served with huge side orders of secrets and lots of weirdness, this might just be for you.