Misato is upset with Shinji for ignoring her orders in the last Angel battle, and he is so overcome by the stress of being an EVA pilot that he runs away. After wandering around Tokyo-3 for several days, Shinji is faced with the choice of quitting or staying in his new home.

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.

Misato has been promoted to Major, but the celebration does not last long. A monstrous Angel appears in Earth orbit right when Gendo and Fuyutsuki are away, leaving her and the children to deal with a colossal kamikaze threatening to drop itself right on top of Tokyo-3.

Kouzou Fuyutsuki is kidnapped and interrogated by Seele, who are horrified over the results of the last encounter with an Angel. He recounts his past, providing flashbacks into the creation of Nerv. The pasts of Misato Katsuragi, Ritsuko Akagi, Rei Ayanami and Yui Ikari are also revealed. Ryouji Kaji, meanwhile, decides to find out the truth, no matter the cost.