
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.

Kaiba recruits further members for his resistance, including Weevil Underwood and Rex Raptor.Ī climactic plot event in both stories occurs when Mokuba is kidnapped, and Scott forces Kaiba to battle against Yugi. After defeating all enemies on the level, Pegasus arrives and asks Kaiba to lead the resistance, as he 'cannot return to the Empire' with a price on his head. Marthis is waiting for him with a unit, and promises the man who brings Kaiba to him anything he wants. However, Kaiba escapes with Mokuba and Bonz. Marthis turns Kaiba in to the Emperor, who sentences him to a public execution. Initially they work for Emperor Haysheen, but Marthis, Kaiba's 'helper', hears Kaiba talking to Pegasus and suspects that Kaiba is a spy for the resistance. Kaiba's storyline features Seto Kaiba and his brother Mokuba Kaiba, who are also trapped in the game. Along the way, the players faces Joey, Tea and Yami Bakura.

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 Haysheen and ultimately stop the plans of the game's designer, Scott Irvine, to control the three Egyptian God cards. The Yugi storyline involves Yugi, Joey, Tristan, Téa and Bakura being invited to the testing of the virtual reality game "Kingdom," created by the company SIC. Seto Kaiba and Yugi Muto, but later the player can get one for Joey Wheeler as well. At first the player can choose between two storylines.
