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At the end Rei says "I don't know what to do," and Shinji says, "I think you should smile," and Rei smiles. ... Afterwards, when I thought about it, I cursed. In short, if she and Shinji completely "communicated" there, then isn't she over with? At that moment, Rei, for me, was finished.
When she smiled, she was already finished, this character." - H. Anno