The Third Angel escapes its confinement and tries to break out of NERV’s arctic Bethany Base, but Mari Illustrious Makinami, a new pilot, launches Evangelion Provisional Unit-05 and destroys the Angel by self-destructing the EVA and safely ejecting at the last moment.
Meanwhile, Shinji Ikari and his father Gendo visit mother and wife Yui’s grave. Shortly after, the Seventh Angel attacks, but is quickly dispatched by the newly arrived Unit-02 and its headstrong pilot, Asuka Langley Shikinami. Ryoji Kaji delivers to Gendo a suitcase containing the mysterious “Key of Nebuchadnezzar” and notes that the destruction of Unit-05 went as planned. Gendo and Kozo Fuyutsuki then visit NERV’s lunar compound, Tabgha Base, to view the construction of Evangelion Mark.06, which is noted as being different from the other EVAs. They are denied permission to land, but briefly see Kaworu Nagisa sitting in space without a space suit. During Gendo’s absence, the Eighth Angel attacks Tokyo-3. Shinji, Asuka, and Rei kill it in an improvised plan devised by Misato Katsuragi. Both Unit-00 and Unit-01 are damaged. Gendo returns and asks to have them both repaired, but SEELE only allows the repair of Unit-01.
In an attempt to heal the relationship between Gendo and Shinji, Rei prepares a dinner party. At the same time, Mari arrives in Tokyo-3. Later, Unit-04 and NERV’s U.S. branch are destroyed during an experiment, prompting the U.S. government to send Unit-03 to Tokyo-3. Due to an international agreement that allows no more than three functioning Evangelions per country at a time, NERV seals away Unit-02 and schedules a test of Unit-03 on the same day as Rei’s dinner party; Asuka volunteers to take Rei’s place as the test pilot, to avoid the party. Once Asuka activates Unit-03, the Ninth Angel possesses the EVA and goes on a rampage. Shinji pilots Unit-01, but refuses to fight the Angel for fear of harming Asuka, who is still trapped inside. Gendo orders the activation of the Dummy System, which makes Unit-01 autonomous, and allows it to savagely destroy Unit-03, crushing the cockpit in its teeth. Emotionally wounded by his father’s cold decision, Shinji leaves NERV.
Asuka survives, but is grievously injured and placed in quarantine for fear of mental contamination by the Angel. Shinji heads out of the city, but the Tenth Angel attacks, so he flees to an emergency shelter. Gendo fails to activate Unit-01 without Shinji, so Mari hijacks Unit-02 and heads out to fight the Angel alone. She removes Unit-02’s limiters and launches an all-out attack, but the Angel severely damages Unit-02. Rei joins the fight with the damaged Unit-00 and charges at the Angel with a missile. The missile detonates, but fails to destroy the Angel. The Angel consumes Unit-00 and integrates it with its own body, allowing it to bypass NERV’s defenses.
Upon seeing Rei consumed along with Unit-00, Shinji rushes to Gendo and asks to pilot Unit-01 again. Shinji fends off the Angel, but before he can defeat it, Unit-01 runs out of power and shuts down. Unit-01 reactivates in berserk mode in response to Shinji’s rage at the loss of Rei. It easily takes down the Angel, and Shinji uses the EVA to reach inside the Angel’s core to save Rei. Unit-01 then starts transcending its physical boundaries to grant Shinji’s wish. At the moment Shinji retrieves Rei, Unit-01 pulls Unit-00’s core out of the Angel. The Angel explodes and its remains, along with Unit-00’s core, are absorbed into Unit-01, fusing them all into one being. Unit-01 then sprouts giant wings of light, and Misato, who has been watching the battle, sees that they are identical to the ones she saw during Second Impact. Ritsuko realizes that the EVA has become a divine being, triggering Third Impact and declares this to be the end of the world.
In a post-credits scene, a spear shoots down from the Moon and impales Unit-01 in the middle of its apotheosis, neutralizing it and stopping Third Impact. Kaworu then descends from the Moon in Mark.06, saying that this time, he will show Shinji true happiness.