The movie opens with a new Evangelion pilot, Mari Illustrious Makinami, being launched in Provisional Unit-05 to destroy the resuscitated skeleton of the Third Angel in its attack on NERV's arctic Bethany Base. She successfully defeats the Angel by self-destructing Unit-05, safely ejecting at the last moment. The film cuts to Shinji Ikari and his father Gendo visiting Yui's grave and the following attack of the Seventh Angel, which is dispatched by the newly arrived Unit-02 and its headstrong pilot, Asuka Langley Shikinami, via an emergency airdrop. Chief Inspector Ryoji Kaji, present at the battle with Unit-05 and arriving alongside Unit-02, delivers a suitcase to Gendo containing an object referred to as the "Key of Nebuchadnezzar." As the movie progresses, Kaji takes the children on a field trip to a research aquarium tasked with resuscitating the ocean ecosystems lost in the Second Impact and all three Evangelions engage the Eighth Angel, showing a previously lacking teamwork. Unit-01 is critically damaged and Unit-00 loses the use of its arms, but SEELE's members declare that only Unit-01 need be repaired and that Unit-00 has served its purpose. Meanwhile, Gendo and Fuyutsuki visit the Tabgha Base on the Moon to view SEELE's progress on the mysterious "Evangelion Mark.06" and while they are denied access, they confirm that Mark.06's construction is fundamentally different from the other Evangelions and briefly even see Kaworu Nagisa sitting on its finger. On Earth, Shinji decides to cook an extra meal for Rei, a gesture that inspires her to invite everyone over for a self-cooked meal during the following week with the hope of improving Shinji's relationship with his father. Meanwhile, Mari arrives in Tokyo-3 by parachute, but accidentally lands on top of Shinji at his school. Soon after, Evangelion Unit-04 and NERV's U.S. branch are destroyed during a test of an experimental engine, driving the U.S. government to send the completed Unit-03 to Tokyo-3. In accordance with the "Vatican Treaty," where Japan and all other nations are forbidden to possess more than three functioning Evangelions at a time, Unit-02 is sealed away. Rei is initially chosen to pilot the new Eva, but Asuka offers to do it for her so she can still host her dinner, earning a rare "thank you" from Rei. The activation of Unit-03, however, goes awry and is revealed to be possessed by the Ninth Angel. As NERV's only functional Evangelion and pilot, Shinji is ordered to destroy it but refuses to fight back for fear of killing Asuka, who is trapped inside. Gendo orders the activation of Unit-01's dummy plug system and the now autonomous Evangelion savagely dispatches the Angel/Unit-03, finally crushing Asuka's entry plug. Shinji is disgusted with his father's actions and, after an unsuccessful assault against NERV headquarters, decides to quit NERV. Asuka is revealed to be alive, but badly wounded and in quarantine for fear of mental contamination by the Angel. After Shinji says his goodbyes and boards a train headed out of the city, the Tenth Angel attacks. As Unit-01 refuses to accept the dummy system, Mari hijacks Unit-02 but fails to defeat the Angel, even after initiating a controlled "berserker" mode by removing Unit-02's limiters. Rei pilots Unit-00, despite its arms being barely functional, and manages to penetrate the Angel's AT-Field with the help off Unit-02 to use an N² mine-armed missile. The Angel emerges unscathed from the blast and consumes Unit-00, with Rei still inside. Mari happens upon Shinji in the damaged Unit-02 and tries to take him to safety, but, upon witnessing the destruction and Unit-00's consumption, he decides to return and pilot Unit-01 once more. While forcing the Angel out of NERV headquarters, Unit-01 runs out of battery power. Resolving to still save Rei, Shinji proceeds to return to a "berserker" mode and defeat the Angel, while making a mental connection within the Angel to save Rei. The result is Unit-01 and Shinji, now fused into one being, combining with the Angel's spattered core, which takes the form of a giant Rei, into a being described as being close to "godhood." Ritsuko declares that the Third Impact is about to occur, while Gendo and Fuyutsuki note this is the result they have hoped for and Kaji comments that SEELE will not be happy with this occurring before the other units are ready. After the credits, the Third Impact is halted by a Lance of Longinus falling from the sky and impaling Unit-01 mid-apotheosis. It is revealed that the lance was thrown by the Mark.06 descending from the moon. Kaworu is revealed to be the pilot and he proclaims to Shinji that "this time, I will make you happy."