Mother is the first other

Origins: the birth of Ayanami Rei

Rei is the first school age person Ikari Shinji meets when he is called to Tokyo-3 by his father. Displaying herself as a strange damsel in distress for Shinji, Rei is the heavily injured replacement pilot for Evangelion Unit 01 when Shinji initially refuses to pilot it at the drop of a hat. Upon seeing her bleeding and in obvious pain, a sign of how much stress and burden she shouldered as the only pilot NERV had before Shinji's arrival, Shinji finally takes a stand, and agrees to get inside a giant robotic creature he had just seen for the first time in his life.

Throughout the series, Shinji holds Rei in high fascination. Rei displays an unusually close bond with Commander Ikari Gendou, Shinji's estranged father. Both Rei and Commander Ikari show each other affection as they have never shown anyone else, and Shinji feels a tinge of jealousy towards Rei, who is able to bond with his own father. Rei herself is a mystery. She rarely speaks and shows little emotional range. It is only in episode 21, in flashbacks, that we find out the connection between Rei and Commander Ikari. Soon after losing his wife, Ikari Yui, to a fatal accident during inital testing on the Evangelion units, Ikari Gendou brings in a strange girl he claims to be a friend's child he is caring for. Dr. Akagi Naoko, Gendou's co-worker and paramour, notices that this child resembles the deceased Yui, and feels a slight suspicion.

The child Rei later wonders off by herself and is discovered by Dr. Akagi, who tries to help Rei find the way back. But the little Rei makes a grave mistake, she repeats a name Gendou used to refer to Akagi Naoko; "old lady." Coupled with her insecurities about Gendou still having feelings for Yui, Dr. Akagi snaps, and chokes Rei with both her hands. Seeing what she had done, Akagi Naoko jumps to her death. Rei would later grow up to be the First Children, destinated pilot of Unit 00.

As it was later revealed, Rei is actually Yui's clone, brought to existence for Commander Ikari's own reasons. This is never literally stated in the entire series, but hints are dropped from many episodes. Shinji himself notices similarities between Rei and his mother, most often by the things Rei sometimes say. Gendou Ikari, Vice Commander Fuyutsuki Kouzou, and Dr. Akagi Naoko's daughter Dr. Akagi Ritsuko are the only people who knew about this initially in the series. It's unlikely anyone else was important enough to be in on the secret, until Ritsuko herself told Shinji and his guardian, Katsuragi Misato.

Fuyutsuki is Commander Ikari's right hand, keeping much of Ikari's secrets for him. In episode 21, during flashbacks, Fuyutsuki is revealed to be Yui's professor, and seems to care a lot for the young Yui. He was troubled by Yui's relationship with the then rebellious Gendou. Yui was a brilliant student who was much of the brainworks behind the development of the Evangelions, but her career was cut short by her death. In one episode, Fuyutsuki speaks a line that is very insightful to what Rei is for them. He calls her the product of his despair and the vessal of Gendou's hope.