Theory and Analysis:Eva-00's Soul

Ritsuko reveals in Episode 23 that in order to function all Evangelions contain a human soul, and it is heavily implied that that soul has to be the mother of the pilot. Eva Unit-01 contains the soul of Shinji's mother Yui, and Eva Unit-02 contains (the maternal part of) Asuka's mother Kyoko. It is implied that all of the other potential Eva pilots in Class 2-A have dead mothers, and that Toji Suzuhara's mother is dead. Thus when Toji becomes the pilot of Eva Unit-03, it's a strong possibility that Toji's mother's soul was inside of it. However, "Rei Ayanami" is a clone of Yui Ikari: Rei does not have a mother. Thus, the identity of the soul contained inside of Eva Unit-00 is a bit of a conundrum, and remains one of the officially unanswered mysteries of the series.

However, evidence and clues as to the identity of the soul in Eva Unit 00 appear several times during the series, particularly in Episode 05, Episode 14, and also Episode 26.

The Evidence

To begin with, a large piece of evidence is that Eva Unit 00 is just a Prototype and often loses control or acts "buggy", implying that there is something different about it. The most obvious answer to that is simply that Rei has no mother, so unlike Shinji and Asuka, her mother's soul cannot be the one in her Eva.

Some have also theorized that Eva Unit 00 simply has no soul inside of it at all; however, Ritsuko seemed clear in Episode 23 that an Evangelion requires a human soul to function, and she said that each Eva contains a human soul.