Grâce à la Leo Corporation, dirigée par Reiji Akaba, de nouvelles avancées technologiques, comme la Solid Vision, un système holographique qui donne vie aux Monstres de Duel, donnant aux Monstres une masse physique et des environnements, laisse les joueurs interagir directement avec eux. Cela a donné naissance aux Action Duel, dans lesquels chaque duelliste peut traverser différents environnements pour localiser des Cartes d'Action pour les aider lors d'un moment critique. L'histoire suit Yûya Sakaki, un élève de seconde année au collège You Show Duel School de la ville de Maiami, dont le père a subitement disparu trois années auparavant alors qu'il devait participer à un duel très important. Durant son combat contre le champion actuel des Action Duel, Strong Nishijima, Yûya éveille un nouveau pouvoir de par le biais de son pendentif, connu comme l'Invocation Pendulum.
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