The young boy Yugi Muto, his friend Joey Wheeler, and other characters from the Yu-Gi-Oh! manga are sucked into a virtual game created by a mad scientist named Scott Irvine, who wants revenge against Seto Kaiba, the CEO of Kaiba Corporation, for firing him. The player has a choice between two scenarios, playing as either Yugi, the main hero of the manga, or Kaiba, his antagonist. Both will eventually have to stop the emperor Heishin from taking over the world, at the same time trying to stop Scott Irvine, and face the creatures that stand on their path to freedom: the Egyptian gods Obelisk, Slifer, and Ra.

Yu-Gi-Oh!: The Falsebound Kingdom is a real-time strategy game with elements of a turn-based RPG. Most of the gameplay consists of navigating troops (commanded by a marshal), battling imperial forces and trying to emerge victorious in order to advance the storyline. Captured towns can be fortified; armories and infirmaries can be built in order to provide supplies and healing for the marshals. The actual battles are handled in a Japanese-style turn-based RPG fashion, the characters exchanging blows until either the player-controlled party or the opponents are defeated.