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.