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.