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Rei Ayanami

Rei, was created by Gendo from a combination of an Angel's DNA (Lilith) and the late Yui Ikari's (Shinji's mother) DNA. In fact, there are numerous clones of her hidden away in Terminal Dogma. These Reis are in fact the key to the "Dummy Plug" system. Her genetic background would explain her distinct similarity in appearance to Yui Ikari. Also, the Rei Ayanami most people see is in fact the second. The first was choked to death by Dr. Naoko Akagi (Ritsuko's mother) when she let loose a startling secret. And so the miraculous recovery wasn't really what it seems. Rei did die, but another Rei then awakened.

Rei seems to smile for only one person: Gendo Ikari, whom she treats like a father. This only appears to complicate the situation between Shinji and his father, yet she seems to show her own affections for Shinji, especially when she helps him in EVA combat (even though she did slap him once when he spoke bad of Gendo).