Yu-Gi-Oh! The Falsebound KingdomYu-Gi-Oh! The Falsebound Kingdom

The Yugi storyline involves Yugi, as well as Joey, Tristan Taylor, and Téa Gardner being invited to the testing of the virtual reality game "Kingdom," created by the company SIC. When they enter the game they soon find themselves trapped within it, and they must summon the help of the game's characters and monsters in order to defeat the game's villain, Emperor Heishin, and ultimately stop the plans of the game's designer, Scott Irvine, to control the three Egyptian God Cards. At one point in the Yugi storyline, some of your friends are brainwashed and you must fight them.

Kaiba's storyline features Seto Kaiba and his brother Mokuba Kaiba, who are also trapped in the game. Initially they work for Emperor Haysheen (Heishin), but Kaiba soon turns against the Empire. A climactic plot event in both stories occurs when Mokuba is kidnapped, and Scott forces Kaiba to battle against Yugi. At the end of both storylines is a segment taking place within a secret room leading from the game's fantasy environment to the inner workings of the computer that is running the game itself. Either team must defeat Scott Irvine as well as the enemy DarkNite, wielder of one of the God Cards (Obelisk the Tormentor in Yugi's story, Slifer the Sky Dragon in Kaiba's). After beating one story, the other storyline becomes harder, with higher level monsters; this is probably due to the ability to carry over monster stats from one story to the next. In this harder mode there is an additional villain, Nitemare, who has the God Card at level 99.

Joey's storyline is a prequel to Yugi's and features some minor characters from the other storylines. Its main villain is Marik Ishtar who uses The Winged Dragon of Ra.