In Yu-Gi-Oh! Dark Duel Stories, the player's goal is to defeat various characters from the Yu-Gi-Oh! manga, anime, and card game, eventually making it to the four Rulers of Ancient Egypt, who have the precious Millennium pieces. Each character must be defeated at least five times in order to get to the next stage. Typically, the goal of a card duel is to reduce the opponent's 8000 life points to zero; however, sometimes a duel can be won by forcing the opponent to run out of cards in their deck, or by having all five pieces of Exodia in one hand.
As usually in Yu-Gi-Oh! games, cards represent monsters: as a general rule, a monster with a higher attack and defense rating emerges victorious. However, in this game elemental affinities play a role as well. For example, a monster of the Aqua element will be beaten by a monster of the Thunder element even if his attack and defense ratings are somewhat higher.
The player can also create his/her own cards by combining card halves that can be obtained after winning a duel. A trade mode and a real-life battle mode (using the link cable) is also available.