You are the adopted brother of Yuma and Kari Tsukumo. And after two years of searching for your parents you return to Heartland City, to find Yuma and all the friends he has made through his dueling, but you also come back to find that Heartland City, and maybe the entire world, is once again in danger from a new chaotic force from another world.

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.