In Paris, a team from the WILLE organization, led by Maya Ibuki, works on a system designed to restore the city to its previous state. Upon being attacked by NERV forces, they are defended by the Wunder fleet and Mari Illustrious Makinami in Unit-08. Mari defeats the attackers, and WILLE restores Paris.
Asuka Langley Shikinami, Rei Ayanami and a still despondent Shinji Ikari are walking across the outskirts of Tokyo-3, arriving at a settlement of survivors, where they encounter Toji Suzuhara, Hikari Horaki and Kensuke Aida, now adults. Toji is a doctor and has a child with Hikari, while Kensuke is a technician, and all are friendly to Shinji. Asuka expresses frustration with Shinji, force-feeding him. As he slowly recovers, Rei explores the village and settles down, working as a farmer. Shinji meets Ryoji Kaji Jr., the son of Misato Katsuragi and the late Ryoji Kaji, who died averting Third Impact. Rei requires constant exposure to LCL and cannot maintain herself, decomposing in Shinji's presence.
Wunder arrives to pick up Asuka, and Shinji decides to go with her, despite protests from the crew. Shinji is placed in isolation. Meanwhile, Kozo Fuyutsuki, distressed over Shinji's treatment by Gendo Ikari in forcing him to experience the same loss as him, helps Gendo restart Unit-13. In response, Wunder heads to Antarctica. Before the mission, Asuka admits her feelings for Shinji but states that she "grew up before him", referring to their actual ages being 28 but bodies being stuck at 14 due to the Curse of Eva, as well as Shinji's suspended animation after Near Third Impact. Shinji apologizes to Asuka for being indecisive in either saving or killing her whilst she was trapped by the Ninth Angel fourteen years previously. Asuka accepts the apology and acknowledges he has matured.
Wunder is attacked by three NERV ships and a swarm of EVA units. Asuka and Mari sortie and move to destroy Unit-13 before it can reactivate. However, Unit-02 refuses to attack Unit-13, forcing Asuka to remove her eyepatch, revealing the Ninth Angel contained within, converting Unit-02 into a "Pseudo-Evolved EVA"-Angel hybrid like Shinji's Unit-01. Unit-13 overpowers and absorbs Unit-02 according to Gendo's plan. Moments before being absorbed, Asuka is approached by her "original", revealing she is a clone of the Shikinami series. Meanwhile, Wunder is attacked by a new EVA, Unit-09A.
In the NERV vessel restraining Wunder, Misato and Ritsuko Akagi confront Gendo. Ritsuko shoots him to no effect, as Gendo has used the Key of Nebuchadnezzar to transcend humanity. He reveals that the purpose of the Shikinami and Ayanami clones is to enact the Human Instrumentality Project, and enters Unit-13. A determined Shinji asks Misato to let him pilot Unit-01. Sakura and Midori Kitakami try to stop Shinji, but Misato protects him and is shot in the process. Misato apologizes to Shinji, saying that she was wrong to blame him and will take responsibility for his actions, as she is still technically his legal guardian. Mari takes Unit-08 and merges it with Units 09A through 12. Inside Unit-01, the original Ayanami clone appears before Shinji, apologizing for not being able to spare him from having to get into an EVA, but Shinji forgives her.
Gendo and Shinji fight in a surreal "Anti Universe", and Gendo shows Shinji an "imaginary Evangelion", a "Black Lilith". Shinji meets Gendo, seeing a vision of his past experiences, including how Yui's loss traumatized him. As a result, Gendo wanted to initiate an "Additional Impact" for a chance to reunite with Yui. Meanwhile, Misato evacuates the crew of Wunder and sacrifices herself and the ship to create the "Lance of Gaius", which gives Shinji the power to rewrite the world. Shinji talks with and provides closure to Gendo; to Asuka, returning her feelings; and to Kaworu Nagisa, revealing the existence of a cycle the cast is trapped in. Kaworu also talks with the elder Kaji, who helps him understand that his own happiness should not be tied to Shinji's.
Shinji says farewell to Rei, deciding upon a complete reset of the world, a "Neon Genesis", without Evangelions. Gendo and Yui sacrifice themselves to spare Shinji from doing so himself, bringing back all humans who were transformed in the Near Third Impact and restoring the world. Shinji waits on a beach as reality resets until Mari comes back to get him, with her "Final Evangelion" being the last to disappear. The children are all present as adults at a train station, and Shinji and Mari leave for a shot at the real world.
