Spoiler Warning
Perhaps the greatest mystery of the Eva pilots is Rei Ayanami. She is the first child designated as an Eva pilot by the Marduk Institute.
The enigmatic first child comes off as very detached from everything except her work as an Eva pilot. When Shinji once asks "Why does she do this?", she answers "I have nothing else." She is dedicated to her work as an Eva pilot and her mission to destroy the angels.
Who is Rei Ayanami, really? Rei is a 14 year old girl, attending classes with other students in Tokyo-3. She comes off as very detached from life. She has attended the school for two years, and yet has no friends at the school. Nor does she seem to want any.
Her air of detachment has led many Evangelion fans to become fascinated with her. Untouched by the ordinary world, there are those who wish to be her. In one episode, when Shinji encounters her coming out of the bath, nude, in her apartment, she is totally unconcerned with covering up, and instead snatches away a pair of Shinji's father's broken glasses that he had picked up in her apartment. She is not even mad about being intruded upon, but later, turns and slaps Shinji when he expresses doubt about his father's work.
The first time that Shinji actually sees Rei smile, it is when Rei is talking with Gendo Ikari about an activation test of her Eva that NERV is about to perform. She is very devoted to Gendo and follows his orders without hesitation. He, in turn, seems very reluctant to risk Rei, and would rather send his own son out to battle the angels. The episodes in which Rei battles angels are ones in which Misato orders her out, and generally Gendo is away.
By the end of the Evangelion TV series, one learns that Rei is a clone, and in fact, is a clone of a being that is a combination of DNA from Yui Ikari (Shinji's mother) and the angel, Lilith. No wonder Gendo seems to tend to her more lovingly than to anyone else.Rei is killed during a battle with the 16th angel in episode 23. In this battle, Asuka is no longer able to even synchronize with her Eva, and Shinji is out of commission and in danger of his life. Rei uses her AT field to neutralize the 16th angel's AT field, and then activates an N2 mine, destroying both of them. Even then, she doesn't stay dead because there are more clone bodies that can be activated and Rei returns in Death, Rebirth, and End of Evangelion. The Rei clone bodies are actually revealed to be part of the dummy plug system, but are destroyed in the final TV episodes by Dr. Ikagi.
When Rei returns in the final Evangelion movies, she is a new clone, and this Rei seems to have a somewhat different personality. With NERV crashing down around them, Gendo takes the new Rei into the heart of NERV where Lilith, the second angel, is crucified to the wall. It is apparent that Gendo expects her to merge with Lilith, taking him with her, but she just says "I'm not your doll," and merges alone. She is reborn as a new angel, a gigantic being that is part of Seele's Human Instrumentality Project, which is supposed to bring all of humanity into a sort of giant Godhead, eliminating all human individuality.
