Summary
| - Volume 6, interspersed through the events portrayed in volume 4, is separated into four different endings each focused on a pair of characters: the first story details Misato and Kaji deciding to continue their long distance relationship, the second story dealing with Ritsuko and Rei dealing with their unrequited loves , the third story is Touji's disappointment at not being able to pilot an EVA and his reunion with Hikari, and the final chapter has Shinji and Asuka getting into a fight and then subsequently understanding what they mean to each other.
- The students learn they are being groomed to pilot Evangelions . Shinji and Rei are deployed to stop an Angel attack where, although he is initially paralysed with fear, Shinji manages to gather his nerves to save Rei and destroy the Angel.
- A new transfer student, Rei, starts at the school. Rei takes a liking to Shinji and confides her feelings to Asuka.
- The series climaxes with an assault on Tokyo-3 by multiple Angels, in which Shinji is ultimately brought into a form of Instrumentality, where he finally admits his feelings for Asuka. Afterwards, the pilots are split up to various training facilities across the world, with the story concluding several years later with them reuniting and unearthing a time capsule they buried together.
- Gendo's life as a troubled junior high student frequently involved in fights is chronicled. His relationship with a young Yui, his meetings with the enigmatic Kaworu, and how their lives change is detailed.
- Kaworu invites Shinji to play at a concert with him. However, Shinji decides to take care of a sick Asuka. Kensuke is able to confess his feelings to Asuka and Rei is able to tell Shinji that she likes him.
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