Shinji Ikari is summoned to Tokyo-3 by his estranged father Gendo, commander of the special agency NERV, to defend the city from a giant Angel by piloting the only weapon capable of battling the monster: Evangelion Unit-01.

Shinji wakes up in the hospital, with no memory of defeating the Angel the night before. Rejected by his father, Misato decides to take Shinji with her to live in her apartment. Later that night, memories of the battle against the Angel come flooding back to Shinji.

Continuing from the previous episode, the Angel Ramiel is drilling down into the GeoFront to attack NERV HQ directly. After Shinji barely survived a direct confrontation with it, Misato devises a plan to have EVA-00 and EVA-01 defeat the Angel by sniping it from a distance using a positronic rifle which requires the total electric output of Japan to power up.

Tokyo-3 comes to a standstill when sabotage knocks out all power, and the personnel must scramble to launch the EVAs manually when an Angel appears in the middle of the blackout.

Misato has been promoted to Major, but the celebration does not last long. A monstrous Angel appears in Earth orbit right when Gendo and Fuyutsuki are away, leaving her and the children to deal with a colossal kamikaze threatening to drop itself right on top of Tokyo-3.

Enraged over Touji's near-death at the hands of his own EVA, Shinji refuses to pilot an Evangelion again and prepares to leave Tokyo-3 for good. He is forced to reconsider that decision when an immensely destructive new Angel attacks just as he is about to leave...

Asuka sinks into deep depression after Arael's mental probing, and is unable to pilot when the new Angel Armisael arrives. Armisael begins physically fusing with EVA-00 and threatens to do the same to EVA-01, prompting Rei to sacrifice herself to save Shinji, only to appear alive soon afterwards.

Too frightened to face Misato or Rei, Shinji runs away yet again, only to meet and strike a friendship with Kaworu Nagisa, the replacement pilot for EVA-02. Kaworu's openness and friendliness provide much-needed comfort for the disturbed Shinji. However, suspicions abound over Kaworu's incredible synchronization abilities.

Instrumentality continues. The focus is primarily on Shinji now, as he learns to accept the individual’s ability to shape their world, and how the self cannot exist without others to define it.