The story takes place in the distant future and focuses on Yuma Tsukumo, a youngster who aspire to become the duelist champion, despite his skills are still on amateur level. Something unexpected happens when he challenges Ryoga Kamishiro to a duel to recover a friend's deck that was stolen from him. During the duel, Yuma is being defeated by Ryoga when the mysterious ghost of Astral appears before him, and aids him to make a comeback victory. Astral explains to Yuma that his mission is to search for his lost memories, that were scattered across the world taking the form of 99 Exceed monsters called "Numbers", and to retrieve them, he must defeat the owners of each Number monster in a duel. Yuma agrees to help him, and thus their journey together begins.