Shinji wakes up in the hospital, with no memory of defeating the Angel the night before. Rejected by his father, Misato decides to take Shinji with her to live in her apartment. Later that night, memories of the battle against the Angel come flooding back to Shinji.

The EVA pilots are disappointed to find out that they are not allowed to go on their class trip to Okinawa, because they have to stay at Tokyo-3 to stay on-call in case of an Angel attack. Meanwhile, a new Angel is discovered in a chrysalis-like developmental stage deep within the magma of the volcano Mount Asama.

In the first half of the episode, a clip show is presented to the Human Instrumentality Committee of Seele, reviewing the attacks of all Angels up to this point. The second part includes a poem in which Rei contemplates her own existence, and a cross-compatibility test between Rei's and Shinji's EVAs.

Shinji achieved an unprecedented 400% synchronization ratio with EVA-01 during the battle with Zeruel, to horrible effect. With the EVA having ascended to the status of a living God and Shinji absorbed inside it, Ritsuko unsuccessfully attempts to recover him.