Shinji begins attending his new school in Tokyo-3, and has a difficult time dealing with the fame of being an Evangelion pilot. Touji Suzuhara, who's little sister was injured in Shinji's fight against the Angel, is angry at Shinji. A new Angel appears, and Shinji must once again pilot EVA-01 to defeat it.

Continuing from the previous episode, the Angel Ramiel is drilling down into the GeoFront to attack NERV HQ directly. After Shinji barely survived a direct confrontation with it, Misato devises a plan to have EVA-00 and EVA-01 defeat the Angel by sniping it from a distance using a positronic rifle which requires the total electric output of Japan to power up.

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.