He wasn't born, at least, he does not remember being born. Books say that it is normal to not remember that, but Shinji remembers everysingle moment since he woke up the first time. Commander Ikari looking at him throught the glass, and Dr. Akagi at his side.
He remembers when he named him 'Shinji' and, when trying to say a word, anything, it came garbled.
Shinji remembers being taught to read, walk, talk, and to take the hits his supperior gives him.
How to obey and how to ignore the calling of underneath Nerv.
Shinji's neck always hurts, he never knows why, Dr. Akagi checks it for him everytime he asks. He stopped asking when Commander Ikari found out and slapped him accross his face and ordered him to never ask her to again.
Shinji also remembers the first time he found out Commander Ikari had a child; everyone at that point already though of him like a shadow, so it was no surprise when Vicecommander Fuyutsuki spoke about a ''Rei'' and how it was her 8th birthday, her name made something on his chest tug. Commander Ikari was stoic as always and commented how its irrelevant for him. Shinji asked Dr. Akagi what does one does on a birthday, he learned about the celebrations and traditions one does in that day. Shinji got to walk to his appartment by himself that day, contemplating if he will get beaten if he asks Commander Ikari to open a communication with her and him so as to develop socialization with his peers like some of his books say.
He never asked, he knew the answer already.
Sodomization was not a common topic on his books at all, but Shinji attained that knowledge by experience when his physical body was about ten years old. It hurt, but it was fine because Commander Ikari said that human closeness was attained through this type of contact, Shinji believed him up until the point that Ikari started calling for 'Yui' whenever he finished.
He's met Yui a few times, she keeps reffering to him as a doll; and how she will dissintegrate him if he dares to pilot her, to keep away from her because he is not part of her but an imprint.
Can't an imprint evolve to be one self?
It's rutine for Shinji to bend over and have his AT field debased by Ikari's lust. Shinji does has a concept of shame, but it is unfelt by him. Apathy is the only real emotion he ever feels. Ego escapes him the longer he lives.
Whenever a piece of him falls, literally, he can get it replaced. He just figures that emotions and memories are too, that's why he does not let himself feel or forget, because if he does it may get replaced too.
Meeting Rei Ikari was odd, she saw him almost pulled apart. Shinji felt sorry for her, for her tears and distress at having to pilot the Eva, but he could also hear Yui's voice, rejoicing having her daughter near.
Rei Ikari won against the expectations of the adults, but Shinji kne that she could do it. If he's not wrong, she was practically bred for it. Granted, Yui had to be awake for it, but she couldn't have done the extend of the destruction without Rei in her.
Shinji observes. He has observed how the Angels call her 'Beloved' and thinks that it fits her. Beloved by a mother who is dead but isn't, by a guardian who can't be himself with her, by a doctor who beds her father, by a friend who hit her in retaliation for his sister when they first met, by another friend who feels more than simple friendship for her, by a girl who wants to reach out but its insecure, by a man who loved her mom and sees echoes of her fondly in her daughter, by Nerv staff who wishes to support her, by a peer who recognizes the loneliness they share and lashes out, by him who knows her but don't, and lastly by a father who is there but should not be; as now, instead of the mother's name he whispers 'Rei' when climaxing.
Shinji's first real, raw emotion after years was defined by 'Dread'.
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Rei Ikari
Fanfiction"Rei, if it was a girl and Shinji, if it was a boy." Yui's baby ended up being a girl. Gendo was ecstatic for a while.