Ayanami Rei 1 was born from science, with no real parents. She was the prduct of cloning sciences that ahd received a jump start after the Second Impact, where most of the human population was killed. Ikari gendo is the closest thing to a parent she has ever known. Ikari treated her as his own child, because in many ways she was; he oversaw her creation, and molded her in the image of his own dead wife, Ikari Shinji's mother. She is half gendo, half his wife; she is not aware of any entity that is "herself". Ayanami Rei died very shortly after she was born, caught in the jealous rage of Dr. Akagi, the original creator of the Magi super-computer system. Furious as Rei related various insults at Dr. Akagi, which she had overheard from Gendo Ikari, Akagi stranged Rei to death and jumped to her death at the bottom of the Nerv Testing Center. Rei was reborn as Ayanami Rei 2, a shell with the memories of the First Ayanami Rei but lack of total understanding of the nature of her death. Her deep seated respect for Gendo remained; he was the only one she would ever fully open up to. Rei was recreated solely to be pilot for Evangelion Unit 00, the second of the Evangelion models to be constructed. The first Evangelion had obliterated itself as Nerv scientists tried to fuse it with Angel technology. Unit 00 was imbued with the essence of Dr. Akagi, and Nerv was unable to completely control this essence. During a synchronization exercise, Unit 00 went berzerk with Rei inside it as it tried desperately to break through it's supports and kill Gendo Ikari. As Evangelion finally shut down and collapsed, Gendo Ikari pried the burning Entry Plug open with his bare hands, leaving permanent marks on his palms. Rei was badly injured, and was unable to pilot as the first Angel finally surfaced and attacked the Geofront. She was spared the responsibility of fighting because of the appearance of Ikari Shinji, the Second Children, pilot of Unit 01, and son to Gendo Ikari. Rei 2 recovered, and began to fight along side Shinji and Asuka Langley, pilot of Eva Unit 02. During one battle, her Eva unit was damaged and had collapsed. Shinji, however, pried open the Entry Plug just as his father did, bursting into tears when he found that Rei was uninjured. It was one of the few times she would ever smile. It was demonstrated that Rei and Shinji had some connection, perhaps even beyond that fo Gendo and Rei, although moreunderstated. This was Rei's innder nature, the essence of Shinji's mother, manifesting itself. Although Shinji was unaware of this, he may have subconciously suspected this; it was Rei he always saw in his visions where he confronted his inner fears. Rei, in a final, last ditch attempt, destroyed herself to save Shinji from a dangerous Angel. Before she died, she said "I want to unite with Shinji-kun", "Unite" meaning to marry/have sexual intercourse with. Ayanami's death remained unknown to the others, however. gendo simply created another Ayanami Rei, and placed her in the Nerv infirmary. When Shinji thanked her for saving him, and asked if she remembered, Rei replied "I don't know. I think I am the third."