The game begins in ancient Egypt, with Prince Atem sneaking out of the palace to see his friends, Jono and Teana, at the dueling grounds. While there, they witness a ceremony performed by the mages, which is darker than the ceremonies that they normally perform. After the ceremony, Atem duels one of the priests, named Seto, and defeats him.
When Atem returns to the palace, he is quickly sent to bed by Simon Muran, his tutor and advisor. As Simon walks away, he is informed by a guard that the high priest Heishin has invaded the palace, using a strange magic. Muran searches for Heishin. When Muran finds him, Heishin tells Muran that he has found the Dark Power, then uses the Millennium Rod to blast Muran. When Heishin finds Atem, he threatens to kill the Egyptian king and queen if he does not hand over the Millennium Puzzle. Muran appears behind Heishin and tells Atem to smash the puzzle. Atem obeys, and Muran seals himself and Atem inside the puzzle, to wait for someone to...
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