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The events of [[Battle City]] have just concluded, and [[Yugi Muto|Yugi]] now owns all three [[Egyptian God]] cards. [[Seto Kaiba]] longs to finally defeat him, and he has a plan. He suspects 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.
Kaiba heads off to Pegasus's castle and challenges him to a [[Duel|duel]]. The stakes are the following: if Pegasus wins, he gets Kaiba's three "[[Blue Eyes White Dragon]]s"; if Kaiba wins, Pegasus hands over the card that can beat the Egyptian Gods. Kaiba wins, and Pegasus must fulfill his wager: he picks up two cards from Pegasus's [[deck]]s. However, Pegasus is confused; he only created ''one'' card to beat the Egyptian Gods, so where did the other card come from?not two...
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 Kaiba|Mokuba]] standing outside. Mokuba says that Kaiba wants Yugi to bring his [[Duel Disk|duel disk]] to the KaibaCorp Duel Dome immediately.
The Pyramid of Light also pulls the souls of Yugi, Joey, and Tristan into Yugi's Millenium Puzzle, where they are chased by [[Mummy (character)|a group of mummies]] controlled by an unknown force...
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 "[[Spinx 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's not done t finished yet. With the Pyramid gone, he summons combines his last trick up his sleeve 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 and , seemingly taking Anubis is seemingly defeatedwith 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.
