Season synopsis
Contains spoilers for this season and earlier seasons.
Fourteen-year-old Shinji Ikari arrives in Tokyo-3 after years apart from his father, Gendo, who commands the defense organization Nerv. Gendo wants him to pilot Evangelion Unit 01 against the Angels attacking the city. Operations officer Misato Katsuragi takes Shinji into her home, while fellow pilots Rei Ayanami and Asuka Langley Soryu become his partners and sources of friction. Training and battles force the teenagers to depend on one another, but Shinji repeatedly questions whether his father values him beyond the machine he operates.
The fighting exposes dangers inside Nerv as well as outside it. When an Angel possesses the Evangelion carrying Shinji's classmate Toji, Shinji refuses to attack; Gendo overrides him with the dummy system, leaving Toji badly injured. Shinji quits, then returns when another Angel threatens headquarters. Unit 01's violent response leaves him temporarily absorbed into the Eva. Asuka's confidence collapses under an Angel's mental assault, and Rei sacrifices her unit to save Shinji. Her apparent return leads to revelations about replacement bodies. Kaworu, Asuka's replacement, offers Shinji affection, but proves to be the final Angel; at Kaworu's request, Shinji kills him to save humanity.
The final two television episodes turn inward as Human Instrumentality confronts the characters with their fears, memories and dependence on other people. Shinji believes that piloting is his only value and that rejection makes him unworthy of existence. An imagined school life shows him a possible self beyond the Eva, and the questioning opens a way to change how he sees himself. He decides that he can learn to accept himself, and familiar faces congratulate him. This psychological conclusion leaves much of the outside world's fate unresolved; it does not include the separate film's battles and ending.