In Neo Kyoto, the citizens rely on the AR game called Build Divide to determine their socioeconomic status; Teruto Kurabe saves Sakura Banka using a mysterious card in his possession, and she enlists his support to help challenge the King.

Teruto reluctantly accepts Sakura’s offer to take part in Rebuild Battles. While they are walking in the city together, she realizes that Teruto is wearing a uniform from Komoku Academy, which is the same school she is a student of. Guessing that Teruto must be a student of Komoku Academy, she takes him there and discovers that he is indeed enrolled at the school. For some reason, one of the only things that Teruto remembers is his strong desire to battle the King. They search the school grounds to find other Build-Divide players, but a second-year middle school student named Hiyori Munenashi suddenly appears before them and…

Hiyori pleads to become Teruto's disciple, and follows Teruto and Sakura around; Teruto is pulled into a crowd of protestors and gets separated from Sakura and Hiyori; a young man named Naomitsu Enjo appears and helps Teruto.

One day, while Teruto is resting in his tent, an injured Naomitsu collapses in front of him. Sakura asks him what happened, and he explains that he just battled Dairo Keisen, also known as the “Card Professor,” who is a researcher of Witchcraft Medicine. Naomitsu fought Keisen because he heard rumors that Keisen was involved in dangerous human experiments and that someone powerful was supporting his shady activities. With each member having their own intentions, Teruto and his team embark on a journey to battle Keisen.