Theory and Analysis:Rei Ayanami (In-Depth)

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Copy/pasta from the Rei Ayanami page; seems T&A Worthy.

It is very probable that part of the soul of "Rei Ayanami" (actually, the soul of the Angel Lilith) from Rei 1 was used as the soul inside of Eva Unit 00. This may explain the difference in personality between Rei 1 and Rei 2, as Rei 2 was "missing" parts of her soul/personality. A corollary of this theory is that after Eva Unit 00 was destroyed, the fraction of the soul of "Rei Ayanami"/Lilith taken for use in Eva 00 was reunited with the whole. This would explain why Rei 3 is more emotional than Rei 2 (crying when she returns to her room, when Rei 2 only cried for the first time right before her death), and is no longer totally obedient to Gendo Ikari (going so far as to break Gendo's glasses from Episode 05 which Rei 2 cherished), her loyalty leaning more towards Shinji.