The Pyramid Of Light
The events of Battle City have just concluded, and Yugi now owns all three Egyptian God cards. As a result of his this and his past victory in the Duelist Kingdom, Yugi has become famous around the world for his masterful strategies and possession of the God cards. Seto Kaiba longs to finally defeat him, but finds every attempt by his research team to formulate a strategy to defeat the Gods fails and overloads their computers. At' wits end, Kaiba decides that since Maximillion Pegasus created the Egyptian God cards, he would have also created a way to beat them, just in case something ever went wrong.
At the same time, Pegasus has a horrible nightmare about the Egyptian God cards becoming trapped in a blue replica of the Millenium Puzzle; despite no longer having a Millenium Item, Pegasus senses something horrible will soon happen.
Kaiba heads off to Pegasus's castle and challenges him to a duel. The stakes are the following: if Pegasus wins, he gets Kaiba's three "Blue-Eyes White Dragons"; if Kaiba wins, Pegasus hands over the card that can beat the Egyptian Gods. They face off in a Duel Arena, which Kaiba mocks Pegasus for still using. Pegasus manages to back Kaiba into a corner with his Toons, but Kaiba turns the tables by calling out his XYZ-Dragon Cannon and destroying Toon World to rid the field of monsters. Kaiba searches a deck Pegasus laid aside, finding two cards. However, Pegasus is confused; he only created one card to beat the Egyptian Gods, not two...
The Pyramid of Light and its Stone Tablet on display at the Domino City museum. Note the three Egyptian Gods Slifer, Ra, and Obelisk engraved on the Tablet
Meanwhile, Yugi Muto and Téa Gardner, seeking refuge from a mob of duelists wanting to face Yugi for the Egyptian Gods, stumble into Domino Museum, where they discover a new attraction on display called the Pyramid of Light, which looks a little like the Millennium Puzzle. Yugi's grandpa, Solomon Muto (who also happens to be visiting the museum), reads an inscription on the side of a sarcophagus (The eye that sees what's yet to come, its vision shall be fulfilled, unless blinded by events predetermined, thus light & shadows both be killed), triggering a strange vision in Yugi's mind concerning his Millennium Puzzle, the Pyramid of Light, Anubis, and Kaiba. After he wakes up, he finds the pyramid stolen, the sarcophagus now empty, and Mokuba standing outside. Mokuba says that Kaiba wants Yugi to bring his duel disk to the KaibaCorp Duel Dome immediately.
Yugi does so, transforming into Yami Yugi on the way, and finds Kaiba ready to duel. Seto asks Mokuba to seal all the exits, forcing Yugi to duel him, but not before Joey Wheeler and Tristan Taylor find their way in to watch.
The duel goes on for what seems like an eternity, and Yugi is starting to suspect that there are dark forces at work - especially when Kaiba activates a Trap Card called the "Pyramid of Light", which not only bears a striking resemblance to its namesake in the museum, but also prevents Yugi from using any of the Egyptian Gods! Before long, Kaiba has his "Blue-Eyes Ultimate Dragon" on the field, but to Yugi's surprise, he sacrifices it to summon a monster known as the "Blue-Eyes Shining Dragon", which is even stronger!
The Pyramid of Light also pulls the souls of Yugi, Joey, and Tristan into Yugi's Millenium Puzzle, where they are chased by a group of mummies controlled by an unknown force...
The power of "Blue-Eyes Shining Dragon" brings Yugi to the verge of defeat, but Kaiba decides to humiliate his rival with the most "perfect" victory possible: wiping him out with his own Egyptian Gods! Having used "Pyramid of Light" to remove the gods from play, he intends to use "Return from the Different Dimension" to get them under his control - but first, he needs to destroy "Pyramid of Light", otherwise it would just destroy the gods again! Kaiba commands his "Blue-Eyes Shining Dragon" to use its "Shining Nova" effect, which allows it to sacrifice itself to destroy anything on the field - and he aims it at the "Pyramid of Light". Suddenly, a ghostly voice calls out, "This I cannot allow!", and the Pyramid stays exactly where it is. Then, a man rises up from behind Kaiba, throws him aside, and takes over the duel himself.
It's Anubis, the Egyptian Lord of the Dead, whom the Pharaoh destroyed 5000 years ago. But now he's back with the Pyramid of Light around his neck and two of his most powerful monsters - "Andro Sphinx" and "Sphinx Teleia"! On top of this, Téa, Joey, Tristan and Yugi are all trapped inside the Millennium Puzzle, leaving the Pharaoh to duel all alone. Putting all his faith into the cards, Yugi draws the "Double Spell" card, which allows him to discard his other spell card to activate "Monster Reborn" from Seto's Graveyard. He uses it to revive "Blue-Eyes Shining Dragon", who then destroys the "Pyramid of Light" (after it was weakened by Yugi from inside the Millennium Puzzle), along with "Andro Sphinx" and "Sphinx Teleia". But Anubis isn't finished yet. With the Pyramid gone, he combines his fallen Sphinxes into a new, even stronger monster - "Theinen the Great Sphinx"! Yugi, however, activates "Reverse of Reverse" to activate Kaiba's "Return from the Different Dimension". The God Monsters return and destroy the Great Sphinx, seemingly taking Anubis with it. But a giant jackal - the ancient Egyptian representation of Anubis, the Lord of the Dead - rises from the remains of the Pyramid!
Kaiba and Yugi join forces, putting all their strength into the "Blue-Eyes Shining Dragon" card, and using Shining Nova to destroy Anubis once and for all. On top of it all, Pegasus, who had earlier arrived via helicopter to help them, gets them out of the explosion in time.