When Yuma Tsukumo sees his friend, Bronk Stone, get beaten in a duel against Shark Kastle, he decides to fight and try to get his friend's deck back. Shark breaks Yuma's key in half however, and the fight looks like it will be tough.

Astral speaks to Yuma and shares advice for how to battle Number monsters, and provides him with a Number monster of his own with which to battle the Number monster that has possessed Shark.

A computer virus is spread throughout the city, causing systems to go haywire. Meanwhile, Astral gets trapped in a world inside Yuma's key, and Yuma later discovers he no longer has his Number card.

Yuma must defeat his maths teacher in a duel before a computer virus planted in the city's computer system spreads.

A classmate named Flip offers Yuma a Xyz monster; Tori and Bronk warn Yuma that Flip is in a lot of trouble.

Yuma must defeat Flip or risk permanently losing his Utopia card.