The game is loosely based on the Wars of the Roses, a series of conflicts fought between the House of Lancaster and House of York for control of England in the 15th century. Yugi Mutou takes on the role of Henry Tudor, the head of the House of Tudor, while Seto Kaiba plays Christian Rosenkreuz, the leader of the Yorkist clan force. Other characters from the series take on the roles and names of those involved in the conflict.
The player controls the "Rose Duelist," who is summoned from an unknown time period to 1485 by a Lancastrian druid to help them defeat the Yorkists and reclaim the throne. Both sides have eight "rose cards" with sorcerous abilities. The Lancastrians want the Yorkists' white rose cards because Seto's forces are using their power to create a barrier that protects their territory, and the Yorkists want the Lancastrians' red rose cards because Seto needs all 16 rose cards to attempt a forbidden "rose summoning" that would give the Yorkists great power. The Rose Duelist also requires all 16 cards to conjure enough power to return to their appropriate time period, forcing the player to choose a side.
If the Lancastrians are sided with, the Rose Duelist obtains the white rose cards by defeating the Yorkist forces, which are represented by antagonists Maximillion Pegasus, Weevil Underwood, and Rex Raptor. The Rose Duelist finally defeats Seto for the final rose card at Stonehenge, but the victory is fleeting as Seto reveals that the power released from their duel (along with all of the rose cards brought to the site by the Rose Duelist) has fulfilled the requirements for the great summoning, and that he feigned allegiance to the Yorkists to force the Lancastrians to summon the Rose Duelist in the first place. Seto then summons Manawyddan fab Llyr, a powerful mythological figure known as the card guardian, whom he intends to use to establish his rule over England. The Rose Duelist defeats Manawyddan fab Llyr and banishes him from the time period, ensuring Lancastrian victory. According to the epilogue, Yugi was crowned King of England, but it is unknown whether the Rose Duelist were ever returned to the time period from which they were summoned.
If the Yorkists are sided with, the Rose Duelist will face Yu-Gi-Oh! series protagonists like Joey Wheeler, Téa Gardner, and Mutou. After collecting all of the rose cards, Seto summons Manawyddan fab Llyr once more at Stonehenge. This time, however, Manawyddan reveals himself to be Nitemare's brother from Yu-Gi-Oh! Forbidden Memories, and he is furious that they summoned his brother in Egypt only to lock him away again. To end the summoning, the Rose Duelist must defeat Manawyddan fab Llyr. After the duel, Seto informs the Rose Duelist that he has been looking for a true card guardian for a long time because an ancestor of his made a pact with one (again, referencing Forbidden Memories). Seto abandons the Rose Duelist with his white rose pendant, and his forces flee England, allowing the Lancastrians to take control of the throne.
