A young Asuka is running home. She's happy because she's been selected as an Eva pilot and wants to tell it to her mother, believing everything will now be okay. She opens the door to her home, only to discover her mother hanging in a noose from the ceiling. With the sound of a slap, the narrative cuts back to the more recent past; In Misato's kitchen, Shinji angrily and desperately tries to tell Asuka that Kaji is dead and won't be coming back. With a face resigned in disbelief she accuses him of lying.
In the present, Asuka lies naked in a bathtub in a ruined and abandoned house on the outskirts of Tokyo-3, with her clothes neatly folded on a chair beside her. She weakly mutters that with a synch rate of 0 she is no longer qualified to be the Second Child; with that her reason to live is gone because no one will look at her now. Someone then enters the ruin and asks, "Are you Asuka Langley Soryu?" Inside NERV's headquarters, Hyuga gets a phone call about the recovery of Asuka. Misato comments that it is unusual for Section 2 to lose track of someone and then be unable to find them for a whole week, and since the finding of Asuka coincides with the arrival of the Fifth Child, she speculates that they did it on purpose.
Back in the apartment, Shinji concludes that there definitely is a connection between Rei, his mother, and the strange presence in Unit-01, but he can't figure out what his father is planning to do with them
Gendo now appears before Ritsuko in her holding cell. She laments the recent death of one of her cats, but he ignores her grief and asks her why she destroyed the Dummy System. "I destroyed Rei," she angrily answers and tells him she no longer feels anything for him and he can just do "whatever you want with my body!" He coldly states "You disappoint me", and she grievously answers that he had no expectations of her to begin with, before he leaves her in the dark. "What am I supposed to do, Mother?" she whispers to the darkness.
Shinji watches the sunset over the lake that now covers the ruins of Toyko-3. He realizes that he has no one he can talk to. Touji and Kensuke has been evacuated to someplace else, he doesn't know where Asuka is, and he finds himself unable to face Misato or Rei, being too scared of both. He then hears someone humming Beethoven's Ode to Joy, and discovers a strange gray haired boy sitting on a chunk of debris nearby. The boy calls song "the greatest achievement of the Lilim culture" and reveals that he already knows who Shinji is. He introduces himself as Kaworu Nagisa, the Fifth Child, and insists right from the get-go that Shinji calls him by his first name. This display of openness makes Shinji blush.
Sitting in her car, Hyuga gives Misato what little information he could find on Kaworu. He was send directly by the Committee and his background is just as blank as Rei's; the only thing that is written down is a birthday, which just so happens to be the same day as the Second Impact. Misato concludes that he is obviously planning something. Hyuga also reveals that he even did a little extra work and hacked into the Intelligence Department's database and found where Ritsuko is being held. He then eagerly asks Misato what their next move regarding Kaworu is going to be, but Misato, amused by his eagerness, tells him to remain calm for now. They will have to see what the Fifth Child is capable of first.
The next day, Kaworu participates in a synch test. He scores an abnormally high synch rate with Unit-02, even without replacing the core of the Eva, which only raises Misato's suspicion of him. After the test Kaworu meets up with Rei, who instantly and uncharacteristically becomes suspicious of him. "You're the same as me," he tells her and refers to the fact that they both have taken the form of Lilim. "Who are you?" Rei asks him distrustfully. Gendo is informed in his office by Fuyutsuki that Kaworu has made contact with Rei, and that the Magi is working hard to come up with information on him.
Back at her apartment, Misato ponders on the lack of information on Kaworu, before noticing that Shinji hasn't returned home, and that she and Pen Pen are alone in the apartment. "I've failed as a guardian," she realizes.
At the Central Dogma station, Shinji is waiting for Kaworu. Kaworu arrives and asks why he is hanging around, and Shinji tells him that he hasn't felt like going home recently. Kaworu then asks him to accompany him in the showers, where they can talk more. Shinji agrees hesitantly. As the two relax in the public bath, Kaworu shares his musings on the nature of mankind with Shinji, finding the paradox of people's need for companionship despite their fear of getting too close to others interesting, and makes several advances towards him, which shocks and embarrass Shinji, but he doesn't shy away from Kaworu. Kaworu eventually asks him if he wants to stay the night at his apartment, and tells him that he holds him in high regard and that he is delicate like glass. Shinji asks what it means, and Kaworu answers: "It means, I love you."
SELEE gathers for another meeting. They have realized that Gendo has turned NERV against them, and declares that they must get the facility back at any cost. Inside the Eva cage, Gendo talks to Unit 01, he addresses it is as "Yui" and tells her that "our wish will be fulfilled." A shot of his ungloved hand reveals the embryonic Adam fused with his flesh. In her apartment, Rei considers her existence, wondering why she is alive again and for what and who's purpose. She then ponders Kaworu's words and realizes that he is right; she senses that the two of them are indeed the same, but she can't explain why. Meanwhile, Misato tells Pen Pen that life in Tokyo-3 has gotten too dangerous, and that she will send him to live with Hikari's family.
Inside Kaworu's apartment, Shinji has settled for sleeping on the floor. Kaworu asks if they should switch places, but Shinji tells him he's fine where he is. He starts telling Kaworu about his problems, wondering all the while why he is sharing them with him. Kaworu smiles sincerely, and tells him: "I might have been born to meet you."
The next morning Kaworu goes to the lake shore. Several SEELE monoliths appear and start briefing him on his mission, telling him that Gendo is trying to acquire the power of God and must be stopped, and that as the spawn of Adam he must remove mankind, the spawn of Lilith, from Earth. Meanwhile Misato spies on the meeting from a mountain some distance away. Unable to see the monoliths, it appears to her as if Kaworu talks to himself. At one point Misato notices that Kaworu looks directly at her, but dismisses the possibility. Meanwhile Kaworu finishes the briefing; "All will be as the Lilim direct it," he comments laconically.
Misato meets up with Hyuga again. Through data he has stolen off Maya, it is revealed that Kaworu can apparently alter his synch rate as he sees fit. Misato decides that her best possibility for some answers comes from Risuko and visits her in her cell. Risuko warns her that the conversation will be recorded, but Misato says she doesn't care and demands answers. Risuko then tells her that the Fifth Child is very possibly the last Angel. Meanwhile Kaworu has entered the Evas' holding cage. He starts levitating upwards, until he comes face to face with Unit 02. "Come with me, Adam's alter ego and servant of the Lilim," he says to the EVA, and in response the creature's eyes light up and it starts moving.
Alarms and confusion breaks out in the control room as Unit-02 starts smashing through the barriers down the shaft to Terminal Dogma. It is quickly confirmed that Asuka still lies sedated in the hospital, so it is concluded that the Fifth Child must be behind it. A blue pattern is detected, and Gendo and Fuyutsuki are shocked by this, not expecting SEELE to actually send an Angel to the Geofront. Gendo deduces that SEELE is once again trying to advance the prophecy. He tells the personnel that the 17th Angel must be kept out of Terminal Dogma by any means necessary. Meanwhile SEELE expects Gendo to send Unit-01 to solve the problem, and hopes that it will succeed, as it will help their scenario.
Shinji, now sitting in Unit-01, refuses to believe that Kaworu is an Angel. But Misato tells him that it is the truth and sends him out. Descending down the shaft he curses Kaworu, accusing him of betraying him, just like his father. He catches up with him, and Kaworu starts attacking him with Unit-02. Shinji mutters a quick "Sorry, Asuka," before drawing Unit 01's knife to counter-attack. During the fight Kaworu shares more of his musings on mankind and their strong urge to survive, and tells Shinji the nature of A.T. Field, revealing that humans also generate them, and that it is what keeps them separated from each other. Meanwhile, Misato and Hyuga prepare the base for self-destruction, declaring it to be better a option than letting the Earth suffer a Third Impact.
Down in the shaft Shinji and Kaworu have reached the last barrier to Terminal Dogma. Kaworu then creates the strongest A.T. Field ever recorded to smash the barrier. This also knocks out all electronic equipment in the area, disabling the self-destruct mechanism. The fighting Evas land in a pool of LCL at the bottom of the shaft, while Kaworu continues to move towards his goal. Shinji tries to stop him, but is held back by Unit-02. Kaworu now opens Heavens Door, the last barrier to the room of the crucified giant. Suddenly an A.T. Field of equal power to Kaworu's appears and channels it out, but it is not a blue pattern. It is revealed to be generated by Rei, who has descended into Terminal Dogma through another shaft.
Kaworu now stands face to face with the crucified giant and identifies it as Adam, wondering if he really wishes to merge with it and destroy all of mankind, before he suddenly realizes that the giant is actually Lilith. Just then, Shinji and Unit-01, having defeated Unit-02, enter the room. He grabs Kaworu who does not resist. Kaworu thanks Shinji for stopping him; "It is my destiny to continue to live, even if it may result in the destruction of humanity," he explains to him, but says that in the end it is his will to die, so that mankind may go on living, and he finishes by telling Shinji to "Erase me from this world." Anguished and scared, Shinji answers: "I don't understand what you are saying!" Kaworu takes a look up at Rei and smiles wistfully before he looks back at Shinji. "Only one life form can be chosen to evade the destruction and inherit the future. And you are not the existence that should die," he explains, before he thanks Shinji for giving his life meaning. After hesitating for a long time, Shinji obliges with Kaworu's wish and crushes him in Unit-01's hand.
As the operation is now over, Gendo watches as Kaworu's blood is washed off Unit-01's hand. Rei stands beside him, in the place of Ritsuko.
At the lake shore, Shinji is in sorrow over the death of Kaworu, telling Misato that he was the only one who ever told him that he loved him. He notices that Kaworu was, in a way, like him and Rei, but also a better person than himself, and he wishes that Kaworu had survived instead of him. Misato tells him that Kaworu with his wish to die willingly gave up his survival and chose a false hope instead, and that Shinji therefore was in his right to kill him. "...How can you be so cruel?" Shinji asks her, utterly crushed.
- Call Back: Kaworu comments that the reason why he can control Unit 02 so easily is because the soul inside it has shut itself away. It seems that the Mind Rape didn't just effect Asuka.
- OOC Is Serious Business: The normally indifferent and stoic Rei immediately puts her guard up around Karowu and eyes him with suspicion.
- Shoo Out the Clowns: Pen Pen's scene.