Mutou Yuugi defeated Pegasus at Duelist Kingdom. Now Pegasus heir, Tenma Yakou, wants revenge. He takes over Kaiba Corporation while Kaiba Seto is in America.

He challenges Yuugi to a duel and wins using a spectacular but mysterious god card, and then kidnaps Anzu! Thus, Yuugi has no choice but to accept Tenma challenge. He must duel against and pass thirteen duel professors at KC to reach Tenma and beat him.