Asuka's trauma leaves her helpless in the face of the latest Angel attack, and Rei must make a terrible sacrifice in order to save NERV. As the Angel contaminates her unit, she self-destructs and destroys the Angel to save Shinji from it. The survivors try to come to terms with the horrible consequences of the latest battle but surprisingly Rei is found alive or is she. A guilt-ridden Ritsuko summons Shinji and Misato to a secret chamber to reveal the truth behind everything. We find out that Rei is a clone of Yui, Shinji's mother, and the true origins of Evangelion. After revealing this to Shinji and Misato, Ritsuko destroys the clones.
After everything, Ritsuko is arrested and locked up for destroying the dummy plugs. Shinji finds himself alone, Asuka won't talk to him, he can't face Rei, and the destruction of most of Tokyo-3 forced his friends to move. The arrival of the Fifth Child is marked by a new friendship between Shinji and the kindred soul in the unearthly Nagisa Kaoru. A battle to the death follows when it turns out that Kaoru is the last Angel. He takes control of Unit 2 and heads for Terminal Dogma. Unit-01 is sent to stop them from reaching Terminal Dogma. Kaoru reaches Terminal Dogma but finds not Adam but Lilith. As his last act, he lets Shinji grab him and after a long pause, Shinji kills Kaoru.