Fourteen years after the cataclysmic Third Impact reshaped life as we know it, Asuka Langley Shikinami and Mari Illustrious Makinami embark on a mission to retrieve a container from Earth's orbit, which holds Evangelion Unit 01 and its pilot, Shinji Ikari. Upon their retrieval efforts, Asuka's actions inadvertently trigger her own Evangelion, unleashing attack drones that are swiftly neutralized by the reactivated Unit 01. Once their task is complete, the mecha deactivates and descends back to Earth, under the watchful eye of Kaworu Nagisa, who reveals he has been awaiting Shinji's return.
Shinji is extracted from Unit 01 and fitted with a lethal explosive collar before he is sent to Captain Misato Katsuragi, who now commands WILLE, an organization determined to dismantle NERV, the paramilitary group responsible for the Evangelion units. As conflicts escalate, Misato activates the flying battleship Wunder, powered by Unit 01, to fend off an onslaught of drones. She cautions Shinji that piloting any Evangelion units comes at a tremendous risk to his life, a direct consequence of the Third Impact, which has also resulted in him and the other pilots not aging. The mysterious Rei Ayanami, another pilot of Unit 01, adds to the multitude of unanswered questions.
In the midst of the turmoil, an Evangelion unit, Mark.09, confronts the Wunder, forcing Shinji to orchestrate a daring escape using Unit 01. With guidance from Rei, he makes his way to the ruins of the NERV headquarters, only to come face to face with his father, Gendo Ikari. Gendo reveals a troubling expectation for Shinji to pilot a new Evangelion, Unit 13, alongside Kaworu. As Shinji connects with Kaworu over their shared passion for piano duets, his relationship with Rei becomes increasingly complex—she lacks memories and individuality, responding only to commands.
Kaworu steps in to enlighten Shinji about the grim aftermath of his awakening of Unit 01, detailing how it inadvertently instigated the Third Impact, forever transforming the world. He also unveils Gendo’s malevolent ambitions to enforce humanity's evolution through an apocalyptic event, aiming to eliminate individuality and reunite with his deceased spouse, Yui Ayanami—a fate sealed within Unit 01’s control system.
As these painful truths unfold, Kozo Fuyutsuki, Gendo's loyal assistant, invites Shinji for a game of shogi, hinting at significant implications regarding Rei and her ties to Shinji’s mother. The reality crashes down on Shinji: Rei is just one of many clones of his mother, with the Rei who saved him being merely the latest version. While Kaworu gains Shinji's trust by removing the explosive collar and placing it on himself, they prepare for their perilous mission centered on the enigmatic Spears of Cassius and Longinus, piloting Unit 13, unaware that the ancient weapons harbor treacherous surprises. As Kaworu, Asuka, and Mari strive to intervene, Shinji's determination drives him to uncover the spears, extracting them from their dormant state.
A chain reaction ignites as Gendo’s directives set off a terrifying series of events, resulting in the decapitation of Mark.06 and the frightening emergence of the Twelfth Angel. This malevolent force is subsequently absorbed by Unit 13, awakening it to disastrous consequences that initiate the Fourth Impact.
As tension spirals out of control, Kaworu's astonishing revelation that he is the First Angel sends shockwaves through the narrative. His subsequent fall to the Thirteenth Angel foreshadows further devastation. Meanwhile, Rei battles to keep Mark.09 in check as it begins to assert its own volition, taking control of Wunder and pursuing dominance.
In a final, desperate attempt to avert disaster, Asuka sacrifices her unit to obliterate Mark.09's autonomous threat. Meanwhile, Mari steps in decisively, ejecting Shinji from Unit 13's cockpit. In a heartbreaking act of bravery, Kaworu takes command of Unit 13, plunging the spears deep into its core before succumbing to the collar's deadly grip.
Left in shock and horror, Shinji watches as his friend and ally meet a tragic end. Asuka then assumes the role of protector, rescuing Shinji from the wreckage and guiding him through the ruins of Tokyo-3, with Rei following closely behind. Amid the chaos, Asuka delivers a powerful admonition to Shinji, emphasizing the critical need to confront one’s problems instead of fleeing from them.
