Theory and Analysis:Rei's relationship with Gendo

Oveview

Rei Ayanami's relationship with Gendo is not completely understood and must remain highly speculative, depending on the few shreds of information revealed in the series. It is known that Rei moved from unwavering loyalty at the beginning of the series to abandoning him for Shinji in the very end, with the consequences that followed.

Gendo and Child Rei

In Episode 21, Rei is seen as a girl of maybe four, and is accompanied by Gendo. This incarnation of Rei has a far more pronounced resemblance to Yui Ikari than the Rei seen in 2015. Rei goes from being a quiet and rather nice four-year old to a mocking little monster when she tells Naoko the truth about Gendo: that he didn't really need her anymore, and called her an "old hag". Angry and completely out of control of her emotions, Naoko strangled the original Rei to death, and, horrified at what she had done, killed herself immediately afterwards.

Whether Gendo, in his trademark callousness, sent Rei 1 to crush Naoko's feelings with the truth, or whether Rei 1 told Naoko her true feelings for her own good is unclear, but Rei 1 appears to be mocking Naoko, or at least happy to tell her the truth. Rei 1 being set against Naoko before her soul was placed inside Eva-00 might explain certain aspects of Eva-00's behavior, namely its tendency to go after Ritsuko when berserk.

If Rei 1 had been set against Naoko on purpose, it is possible that she, as Eva-00's resident soul, would want to take revenge against Ritsuko, the daughter of the person who killed her, and whom she might have associated with Naoko. In addition, as the chief scientist of Project E, she probably blamed Ritsuko for placing her soul in an Eva. She might have rejected Rei 2 as not being a part of her, or because she found something inside Rei 2's mind revolting, and might have tried keeping Shinji inside(Possibly, as Ritsuko says, to absorb him), because she might have mistaken him for Gendo. That Rei 2 sees Gendo just before Eva-00 explodes in Episode 23 might be due to the feelings for Gendo that both Rei clones share.

Rei 2

Rei 2 is perhaps the most loyal of the Rei clones towards Gendo, and Gendo once does demonstrate his feelings for Rei by going and personally rescuing her from the superheated entry plug, burning his own hands in the process.

Rei 3

Unlike Rei 2, Rei 3 appears to possess the full soul of Lilith, and it is probable that she has the memories of Rei 1 as well. She seems more understanding of the fact that Gendo used her and would use her again for his own purposes, and so diverted her loyalty to Shinji instead.