The story takes place in the near future in a city called Heartland. Tsukumo Yuuma is a young duelist who strives to become the Duel Monsters champion, despite being an amateur. One day, during a duel with a school bully, a mysterious spirit called Astral appears before Yuuma, and helps him to win. Astral then explains to Yuuma that he is searching for his lost memories, which have been transformed into 99 "Xyz Monster" cards called "Numbers" and have been scattered across the globe. The "Numbers" have the ability to possess the duelists who own them and bring out their darkest desires. In order to recover his memories, and collect the "Numbers" cards, Astral teams up with Yuuma.

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Same setting: Yuu Gi Ou 5D's
Sequel: Yuu Gi Ou! Zexal Second
Same setting: Yuu Gi Ou: Arc-V