The series is set in the distant future in which the Earth is split in two. The southern hemisphere is placed in another dimension while the inhabitants of the northern hemisphere are able to morph into beast-like humanoids. Eventually the humans of the southern hemisphere, led by Uranus, attack the Beasts. The Three Beasts, Wan Derbard (Wan Dabadadatta) of the Tiger Tribe, Bud Mint (Baado Mint) of the Bird Tribe, and Mei Mer (Mei Mah) of the Mermaid Tribe, are taken prisoner along with Mei Mer's companion Tuttle Millen (Mekka Mannen, also of the Mermaid tribe), but manage to escape thanks to a little girl named Yuuni Charm Password. Together they seek Gaia, which they believe to be a fabulous treasure, but they are pursued by Uranus's minions : V-Darn the vicious mage-knight, V-Sion the warrior woman and Akumako, V-Darn's sadistic imp-like partner.

Following their heroic efforts at Walter Park, the students of the misfit class return to Babyls Demon School after their summer vacation. What awaits them is not only adoration and admiration but also the shocking revelation that, in order to stay in the luxurious Royal One classroom, the entire class must be promoted to Dalet rank before entering the second year. As the Harvest and Music Festivals are right around the corner, there seem to be ample opportunities to rank up. Doing so will not be simple, however, as no class thus far has managed to accomplish such a feat. Hoping to give the misfit class a chance to achieve the improbable, the school appoints special tutors to aid in confronting the challenges that lie ahead. With his sights set beyond Dalet, Iruma Suzuki decides to take strides toward the goal of ranking up, starting with gaining acknowledgement from his special tutor: the short-tempered and selfish Bachiko Barbatos.

Bullies often target someone frail and weak—someone exactly like Yuugi Mutou. His beautiful childhood friend, Anzu Mazaki, is always there to stand up for him, but he can't depend on her forever. Katsuya Jonouchi, who is almost always accompanied by his verbal sparring partner Hiroto Honda, doesn't seem like a bad person either, despite always bringing Yuugi trouble. But most of all, Yuugi wishes for a true friend who understands him and would never betray him. Yuugi treasures his Millennium Puzzle, an ancient Egyptian artifact that was brought into his grandfather's game shop. Believing that solving the puzzle will grant him his wish, he completes the puzzle, unleashing a new personality within him—the soul of the "King of Games." Dark, twisted, strong, and reliable, the new personality named Yami Yuugi is the exact opposite of Yuugi. Upon any injustice toward him, Yami Yuugi takes over Yuugi's body and forces the opponent into a "Shadow Game." The stakes are high as whoever loses shall have a taste of the darkness that resides within their own heart. [Written by MAL Rewrite]