The events of Battle City and the Paradise arcs have just concluded, and Yugi now owns all three Egyptian God Cards. Seto Kaiba longs to finally defeat Yugi, and he suspects that since Maximillion Pegasus created the Egyptian God Cards, he would have also created a way to beat them. Kaiba heads off to Pegasus' retreat castle to find the card. Meanwhile a shadowy being breaks into Pegasus' safe and adds a card to the deck hidden inside. Kaiba arrives
and challenges Pegasus to a duel, wagering his Blue-Eyes White Dragons for Pegasus' card that can beat the Egyptian Gods. Kaiba wins, and Pegasus' allows him to search his Deck for the card. To Pegasus' surprise Kaiba finds two cards, capable of defeating the God Cards. Kaiba leaves ignoring Pegasus' claims that there should only have been one card.
Meanwhile, Joey and Tristan hold off a mob of duelists wanting to duel Yugi for the Egyptian Gods (until Joey ends up dueling with and defeating all of them), with Yugi and Téa seeking refuge in Domino Museum, where they meet up with Yugi's Grandpa. They discover a new attraction on display, the Pyramid of Light, which resembles the Millennium Puzzle. Once Grandpa reads an inscription on the side of a sarcophagus, also part of the exhibit, Yugi has a strange vision about Kaiba. They wake up to find the pyramid stolen, the sarcophagus empty, Yugi wanting Téa to read him an ancient story of the pharaoh's past, and Mokuba standing outside. Mokuba says that Kaiba wants Yugi to come to the KaibaCorp Duel Dome immediately. Yugi does so, transforming into the Pharaoh on the way, and finds Kaiba ready to duel. He seals all the exits, forcing Yugi to duel him; Joey and Tristan, who have been chasing Yugi to see what he's up to, are also trapped.
During the duel, Yugi is starting to suspect that there are dark forces at work - especially when Kaiba activates a trap card called thePyramid of Light, which not only bears a striking resemblance to the pyramid in the museum, but also removes the Egyptian Gods from play; it also sucks Yugi, Joey and Tristan's souls into the Millennium Puzzle, and later Téa as well. During the duel, as Yugi and Kaiba lose Life Points, they begin to lose their own life force as well. Before long, Kaiba has his Blue-Eyes Ultimate Dragon on the field, but to Yugi's surprise, he sacrifices it to summon an even stronger monster, the Blue-Eyes Shining Dragon. Kaiba wants to humiliate Yugi by wiping him out with his own Egyptian Gods; since Pyramid of Light removed the Gods from play, Kaiba plans to play Return from the Different Dimension to get them under his control. Kaiba commands his Shining Dragon to use its special effect, which allows it to sacrifice itself to destroy the Pyramid of Light. Suddenly, a ghostly voice calls out and the effect is canceled. Anubis, the Egyptian Lord of the Dead whom the Pharaoh destroyed 5,000 years ago, is resurrected by Yugi's ebbing life force and rises up from behind Kaiba, throwing him aside and taking over the duel himself, all in the hopes of having his revenge against the Pharaoh.
Putting his faith into the cards, Yugi draws the Double Spell card, which allows him to discard a card to activate Monster Reborn from the graveyard. He uses it to revive Blue-Eyes Shining Dragon and destroys the Pyramid of Light, after it is weakened by Yugi inside the Millennium Puzzle, which also releases him, Joey, Tristan and Téa. Anubis then summons Theinen the Great Sphinx with the Pyramid of Light around his neck. Yugi then uses the Reverse of Reverse trap card to use the Return from the Different Dimension placed face-down by Kaiba to return the Egyptian God Cards and use them to defeat Anubis's monster. Anubis is seemingly defeated, but a giant jackal arises from the remains of the Pyramid and attempts to kill Yugi and his friends. Kaiba and Yugi join forces and summon the Blue-Eyes Shining Dragon, which destroys Anubis once and for all.
