Shinji Ikari is summoned to Tokyo-3 by his estranged father Gendo, commander of the special agency NERV, to defend the city from a giant Angel by piloting the only weapon capable of battling the monster: Evangelion Unit-01.

Shinji wakes up in the hospital, with no memory of defeating the Angel the night before. Rejected by his father, Misato decides to take Shinji with her to live in her apartment. Later that night, memories of the battle against the Angel come flooding back to Shinji.