A masked man, known as the Controller, has plucked the major focal points of Duel Monsters history and gathered up the biggest villains from each timeline to destroy the history of Duel Monsters itself! Now with the help of their friends and allies, Yugi Muto, Jaden Yuki, Yusei Fudo and Yuma Tsukumo join forces to prevent the threat from destroying the game they love!

After his older sister's death, an aspiring 15-year-old cartoonist runs away from home, wishing for a better chance at life. A cyclone sends him to the most unlikeliest of all places: Equestria!