Unit 00 - Prototype

After several mistakes, bioengineering finally managed to create a stable prototype, Unit-00. But it proved evenly difficult to synchronize the EVA to his/her new pilot, Ayanami Rei.
EVA went berserk in the first tests, trying to kill Rei and, oddly, Ikari Gendo, who knowingly smiled when he realized that.
Originally outfitted in orange and without the shoulder-blades, Unit-00 was heavily damaged in episode 5, while protecting Unit-01 against Ramiel's attack. After that, the armor was painted blue and shoulder-blades were added.
The soul inside Unit-00 could be the soul of Akagi Naoko, Ritsuko's mother and inventor of the MAGI-system. She had an affair with Gendo, but when she found out that Rei was a clone of Ikari's dead wife Yui, she killed the first Rei and then commited suicide. This explains why Unit-00 tried to kill Gendo (betrayed love), but why did it attack Ritsuko then?.
Another possibility is that the soul of Lilith was implanted in Unit-00 (and maybe Rei as well).
This would explain why Unit-00 attacked Gendo (responsible for "her" suffering) and Ritsuko (daughter of the scientist that developed the according technology).
As well would this explain why Rei, when entering the body of Lilith in End of Evangelion said "I'm home" and was greeted with "welcome back", marking the point when Lilith's body was reunited with her soul-fragments.
The physical appearance of Unit-00 seems to be modeled after the first baron of hell, who featured one giant eye.