Years have passed after Yugi's adventures and now it's Yuki Judai's turn. Yuki Judai is a new student in the school Duel Academy, a school dedicated to teach duelist the basics and advanced techniques. Judai is determined to be world's #1 duelist, accepting challenges from his rivals (and friends). Although the manga is based on the anime, the story is really different and unrelated.

Mukae Jinki have gathered 15 Fighters, and One who have chosen from winning all the Shop Tournaments. These 16 fighters will fight for the throne to be the strongest, as the Curtain for the Second Deluxe Opens!! Who will be the one to Control the fight, who will be the one to win!?