Rei 3

"Rei 3" is the third Rei Ayanami clone, which appears from the middle of Episode 23 through The End of Evangelion, where she merges with Adam and Lilith.

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. For further analysis, see: "The Soul in Evangelion Unit-00". 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 Ikari.

Notes

• "Rei 3" is a fan-created designation, sometimes written as "Rei III".
• When Ritsuko Akagi destroys the Dummy Plug "parts" factory which is really a cloning center for creating new Rei clones, her controller's display lists the inanimate future Rei-clones starting with "Rei 4". However, all of these prospective future clones were destroyed by Ritsuko, before Rei's (Lilith's) soul was ever transfered into them, and they were simply soul-less husks.