Legend says that the enigmatic Millennium Puzzle will grant one wish to whoever deciphers its ancient secrets. Upon solving it, high school student Yuugi Mutou unleashes "another Yuugi," a peculiar presence contained inside. Now, whenever he is faced with a dilemma, this mysterious alter ego makes an appearance and aids him in his troubles.

Wishing to unravel the mystery behind this strange spirit, Yuugi and his companions find themselves competing with several opponents in "Duel Monsters," a challenging card game used by people seeking to steal the Millennium Puzzle in a desperate attempt to harness the great power within. As the questions pile on, it is not long before they figure out that there is more than pride on the line in these duels.