Scarred by Second Impact, the Fourth Angel attacks Tokyo III and the fate of humanity is left in the hands of the NERV Special Government Agency.  Young Shinji Ikari is forced to pilot EVA-01.  He and EVA-00 pilot Rei Ayanami are tasked with fighting, but EVA-01 is damaged by the Sixth Angel.  Misato Katsuragi devises a plan to focus all of Japan's electricity into EVA-01's positron cannon to defeat the Angel.

Shinji Ikari has finally woken up fourteen years after causing the Third Impact. He hasn't aged at all since the incident, but everything else has changed. The earth is in ruins. The people he once protected treat him like a prisoner and threaten to kill him if he pilots another Eva. At NERV headquarters, Shinji meets pianist Kaworu. As the boys bond, the organization's true mission comes into focus. Lost in a labyrinth of deception, Shinji careens toward a mental breakdown that could bring about the end of humanity.