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.