Introducing Shinji Ikari as a school boy at NERV Catholic School along with Asuka and Rei. After seeing Rei with a mysterious boy in an alley way one night—who later turns out to be Kaworu—Shinji is exposed to the realities about the Angels, receives his EVA, and joins the group of teenage children in their mission to fight them.
Gendo Ikari reveals his true intent is to bring back whatever version of Yui he can. Rei refuses to become the spare and so Gendo shoots her, saying as he does that he can now use Shinji as an alternative. Kaworu tells the other characters of his Angel status, but falls victim to NERV's new "anti angel" weapon. However he manages to recover sufficiently to rescue Shinji from Gendo's plan. In the coma induced scene witnessed by Shinji next Kaworu states that it was Shinji who made him "not want to destroy mankind." The Manga ends with Rei, Asuka, and Shinji returning to school.