*Taking place in the near future in a place called Heartland City, the story focuses on Yuma Tsukumo, a young duelist who strives to become the Duel Monsters champion, despite being an amateur. One day, during a duel with a rival named Shark, a mysterious spirit called Astral appears before him, and helps him to win.

Astral explains to Yuma he is searching for his lost memories, which have been transformed into 100 Xyz Monster cards called Numbers. which 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, Astral teams up with Yuma to recover the Number cards. After coming up against a boy named Kite Tenjo for the second time, who is hunting the Numbers, Yuma and Astral gain the ability to combine their forces using the power of ZEXAL. Entering the World Duel Carnival tournament, Yuma finds himself up against various rivals, including the vengeance-seeking Vetrix and the maniacal Dr. Faker, who want the Numbers for their own gain.*