Ritsuko briefs Shinji on the real nature of Second Impact, the Angels, and the Evangelions' mission to defeat them. Misato and Ritsuko attend the public demonstration of a new Angel-fighting robot, Jet Alone, built by a rival defense contractor to NERV. However, the nuclear-powered robot quickly runs out of control, and Shinji must use EVA Unit 01 to load Misato onto Jet Alone so she can she can enter in its automatic shutdown code, before it melts down in a nuclear explosion.

A routine test involving the EVA pilots turns into a struggle for survival when a wholly new type of Angel appears and spreads inside NERV HQ. This new, computer-like angel threatens to set off the self-destruct for the entire facility, leaving Dr. Ritsuko Akagi in a race against time to save the GeoFront and destroy the Angel.

Evangelion Unit-03 arrives from the United States. However, its activation experiment brings out NERV's worst nightmare when it turns out to have been infected by the Thirteenth Angel. The other EVAs are dispatched to battle the Angel-infected abomination... even at the risk of killing its helpless pilot.