Contains spoilers for this episode and earlier episodes.
Asuka is found in an abandoned building after losing the ability to pilot, and Nerv places her in medical care. Her replacement, Kaworu Nagisa, arrives directly from the committee. Shinji encounters him beside the ruined city and responds to his unusual warmth at a time when his other relationships have become strained or distant. Kaworu's synchronization with Unit-02 amazes the staff, while Misato investigates his sparse records. He speaks to Rei as though he recognizes something shared between them. With Shinji, he offers affection and a chance to talk about loneliness and his father, giving the exhausted pilot a connection he has badly needed.
Kaworu then activates Unit-02 without entering its cockpit and descends toward Terminal Dogma. Nerv identifies him as an Angel, and Shinji pursues in Unit-01, feeling betrayed by the boy he trusted. Unit-02 blocks his path while Kaworu continues toward the crucified giant below. Misato prepares for the possibility that headquarters must be destroyed to prevent another catastrophe. At the destination, Kaworu realizes that the being is Lilith rather than Adam. Shinji defeats Unit-02 and captures him. Kaworu asks Shinji to end his life so humanity can continue, making the choice painfully personal. Shinji eventually kills him, then struggles with the loss as Misato tries to convince him that he acted correctly.