Shinji Ikari just woke up in his Eva unit fourteen years after starting the Third Impact. He hasn't aged, but everything else has changed. The earth is in ruins. Rei is missing. The people he once protected treat him like a prisoner and threaten to kill him if he pilots another Eva.

When he escapes to the remains of NERV headquarters, Shinji meets pianist Kaworu, who is destined to be Shinji's co-pilot in a new dual-cockpit Eva. As the boys bond, NERV's true mission begins to come into focus. Lost in a labyrinth of deception, Shinji careens toward a mental breakdown that could bring about the end of humanity.