After the catastrophe "Second Impact" that struck the world, the world was rebuilt on the ruins. 14-year-old boy Shinji Ikari was called to the third new Tokyo by his father Ikari Gento. He thought he would be greeted by his father, but he saw a giant creature called "Angel" exchanging fire with the army. In a critical situation, Katsunari Misato of the secret agency NERV rescued Shinji and took him to the NERV headquarters led by Ikari Gento. But what greeted Shinji was his father's cold order: drive a giant humanoid robot called "EVA" to fight the Angel. Shinji, who had already refused, decided to obey his father's order after seeing the seriously injured substitute pilot Rei Ayanami. In this way, Shinji, who had never received combat training, prepared to drive EVA Unit-01 to fight the Angel. The Angels kept attacking, the unknown Rei Ayanami, and the pilot Asuka Langley Soryu from Germany, the 14-year-old boy had to face challenges far beyond his ability. And Ikari Gento watched everything calmly, and a mysterious plan called "Human Instrumentality Project" was being implemented according to his plan.