Shortly after the conclusion of the Battle City tournament, Yugi Muto, the holder of the three powerful Egyptian God Cards, finds his victory shadowed by a new and ancient threat. Beneath the sands of Egypt, an evil spirit known as Anubis, the Lord of the Dead, has awakened. Centuries ago, this entity was defeated by Yugis mysterious alter ego, the ancient Pharaoh, and now Anubis has returned, wielding the power of a never-before-seen eighth Millennium Item, to exact his revenge and plunge the modern world into chaos.

The story is set in Domino City, where Yugi and his friends Téa, Joey, and Tristan seek refuge from a mob of duelists at the Domino City Museum. There, they discover an exhibit featuring a strange artifact called the Pyramid of Light, which bears an unsettling resemblance to Yugis own Millennium Puzzle. Meanwhile, Yugis arch-rival, Seto Kaiba, remains obsessed with finally defeating the Pharaoh. Believing that the creator of Duel Monsters, Maximillion Pegasus, must have designed a card capable of countering the God Cards, Kaiba forces Pegasus into a duel and claims his prize: two specific cards designed to neutralize Yugis ultimate monsters.

When the Pyramid of Light is stolen from the museum and a sarcophagus is found empty, Yugi is summoned by Kaiba to a duel at the KaibaCorp Duel Dome. As the duel commences, Kaiba activates a trap card that mirrors the stolen artifact, known as the Pyramid of Light. This trap prevents Yugi from summoning his Egyptian God Cards, forcing him to rely on different strategies. Kaiba unleashes his Blue-Eyes Shining Dragon, a monster even more powerful than the Blue-Eyes Ultimate Dragon, and seems on the verge of victory. However, before he can strike the final blow, the spirit of Anubis emerges from the shadows, casting Kaiba aside and taking control of the duel himself.

Donning the Pyramid of Light, Anubis traps Yugis friends inside the Millennium Puzzle and summons his own colossal monster, Theinen the Great Sphinx, leaving the Pharaoh to face the ancient evil alone. The narrative arc focuses on the Pharaohs struggle to overcome a foe that has specifically designed his power to nullify the Egyptian Gods. In a final gambit, the Pharaoh places his faith in the heart of the cards, using a combination of Double Spell and Monster Reborn to resurrect the Blue-Eyes Shining Dragon. With this dragon's power, he destroys the Pyramid of Light, which in turn banishes Anubis and his Sphinx, saving his friends and restoring peace.