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The story takes place soon after the Final Round of Battle City.
I2 (Industrial Illusions), Pegasus' former company, take over the duel ring server of KaibaCorp. The leader of I2 at that time is Yako Tenma, the adopted son of Pegasus. With the main computer, Yakou projects a hologram of his body, then meets Yugi and accuses him of killing Pegasus through their duel (not realizing it was Yami Bakura that ultimately killed him). He then challenges Yugi, boasting about the "Wicked Gods" that shall punish Yugi. Yugi then Summons "Slifer the Sky Dragon", but then Yakou summons "The Wicked Avatar", whose form is similar to Ra's sphere mode. It takes the shape and attack points of the strongest monster on the field, so it therefore becomes a twisted replica of "Slifer". It always has one more attack point than the strongest monster, so it is therefore able to defeat it.
After the duel ends Téa Gardner appears to vanish, and it's revealed she had already been kidnapped, and is being held at KaibaCorp, as Tenma needs her for his "R.A. Project". Tenma challenges Yugi to stop him, and Yugi rushes to the tower alongside Joey and Tristan. The tower of guarded by ten Card Professors, each of which has a card key that will get him further into the tower. The first Card Professor, Deschutes Lew, hands Yugi a Soul Prison card. Should he lose a duel, he must hand this card over to whoever beat him, and he will be unable to continue his journey through the tower.
Both Yugi and Joey successfully defeat some of the Card Professors, though Yugi is eventually separated from Joey and Tristan. Yako Tenma eventually approaches him, with Téa's soul on the line. However, should Yugi lose, he must hand over all three of the Egyptian Gods. Tenma reveals the second of the "Wicked Gods", "The Wicked Dreadroot", but Yugi successfully defeats it with "Arcana Knight Joker". After the duel, it becomes clear that Yugi wasn't dueling Yako Tenma, but his twin brother, Gekkou Tenma. Yakou had taken over Gekkou's mind in order to duel Yugi. Tenma reveals the goal of his "R.A. Project" (short for "Rebirth of Avatar") is to call the soul of Pegasus back from the dead in Téa's body.
Gekkou regains his mind, and reveals that he opposes his brother's plan. He also reveals that Yugi can communicate with Téa by placing the "Soul Prison" card on his Duel Disk. Seto and Mokuba Kaiba soon arrive back at KaibaCorp via their jet in order to retake KaibaCorp. Yakou had told Kaiba not to interfere, and promised that return of the server after his plan was completed. Kaiba defeats a Card Professor to gain access to the tower, but by the end of the duel Mokuba has hacked into the security system, so they don't need the card key.
Yugi questions Gekkou as why Téa was chosen. The prerequisites for placing a soul in another body are complicated. Duelists tend to fight back, so a non-duelist had to be used. The person must be healthy, and they must be a family member or friend of the enemy. Téa was chosen as she met all these requirements. He also reveals that the man who told Yakou what happened to Pegasus, and insinuated Yugi's involvement in the incident was Bandit Keith. They soon meet with Keith, and Gekkou himself defeats another Card Professor.
Kaiba arrives at the top of the tower, and duels Yakou in an attempt to regain his company. However, Gekkou defeats him with a combination of "The Wicked Avatar" and "The Wicked Dreadroot". Yakou had hoped to use this duel to call Pegasus' soul, but Kaiba is able to stop him with an override function. The final two Card Professors, Depre Scott and Richie Merced, duel Yugi and Gekkou. Yugi (without help from Yami Yugi) defeats Scott using "Toy Magician". Gekkou loses to Richie, however, but Joey has already found Téa, so it hardly matters. Confusing Gekkou for Yakoy, Joey assaults him, but is stopped by Yugi and apologizes. Yugi, Gekkou and Tristan continue into the tower, while Joey duels Bandit Keith, whom he defeats with "Gearfried the Iron Knight", freeing Keith from his fear in the process.
Yugi finally duels Yakou once more, and is able to defeat "The Wicked Avatar" using "Obelisk the Tormentor" and "Divine Evolution". Yakou is frustrated, but continues the duel with encouragement from Gekkou and his memories of Pegasus. Yugi ultimately defeats him, and control of KaibaCorp returns to Kaiba, while Yugi is reunited with Téa.
Yu-Gi-Oh! The Movie: Pyramid of Light
In Yu-Gi-Oh! The Movie: Pyramid of Light, the events of Battle City have just concluded, and 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.
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. It's called the Pyramid of Light, and it 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 Yugi to have a strange vision about his Millennium Puzzle, the Pyramid of Light, Anubis, and Kaiba. After he wakes up, he finds the pyramid has been stolen, the sarcophagus is now empty, and Mokuba is standing outside. Mokuba says that Kaiba wants Yugi to bring his Duel Disk to the KaibaCorp Duel Dome immediately.
Yugi does so, switching with 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. Kaiba has obtained the card that defeat the Gods from Pegasus.
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 also bares a striking resemblance to the pyramid in the museum, but also prevents Yugi from Summoning any Egyptian Gods! Before long, Kaiba has his "Blue-Eyes Ultimate Dragon" on the field, but to Yugi's surprise, he Tributes it to summon a monster known as the "Blue-Eyes Shining Dragon", which is even stronger!
Kaiba could win the duel there and then, but he wants to humiliate Yugi by wiping him out with his own Egyptian Gods! His "Pyramid of Light" removed the Gods from play, and he wants to play "Return from the Different Dimension" to get them under his control. Of course, to do that, he needs to destroy his "Pyramid of Light" first, otherwise it would just destroy the Gods again. Kaiba commands his "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. And he has the Pyramid of Light around his neck.
It's Anubis, the Egyptian Lord of the Dead, whom the Pharaoh destroyed 5000 years ago. But now he's back with his secret weapon - "Theinen the Great Sphinx"! 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 the Kaiba's Graveyard. He uses it to revive "Blue-Eyes Shining Dragon", who can then destroy the "Pyramid of Light" (after it was weakened by Yugi from inside the Millennium Puzzle). With the Pyramid gone so is the "Great Sphinx", and Anubis is seemingly defeated. But, a giant Jackal arises from the remains of the Pyramid: it is the ancient Egyptian representation of Anubis the Lord of the Dead.
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 was back to help them, and gets them out of the explosion in time.
Yu-Gi-Oh! Capsule Monsters
In Yu-Gi-Oh! Capsule Monsters, Yugi had strange recurring nightmares about the Pharaoh being captured by an evil monster with glowing red eyes. This upsets him since his Millennium Puzzle always starts acting in a strange manner afterwards.
As if this wasn't bad enough, Solomon Muto, Yugi's grandfather, recently went on a "secret expedition" and was supposed to be back already. Yugi is worried about the fact that Solomon is missing, but when Joey Wheeler wins a trip for four to India, Yugi's mind drifts off of the idea.
Meanwhile, there is a new game on the block; the Capsule Monsters board game is the new fad in the Duel Monsters craze, and Yugi has already taken the opportunity to learn the rules of the game. When Joey breaks the news about the trip, Yugi and his friends could not contain their excitement. Yugi, Tristan Taylor, and Téa Gardner agree to take Joey's other three tickets.
Just when the plane approached its final destination, the engines cut out and the aircraft crash lands in a mysterious forest. After Yugi and his friends evacuate from the aircraft, they find a man who says his name is Dr. Alex Brisbane.
When Yugi lets slip to Brisbane that he is Solomon Muto's grandson, Brisbane tells him that he's a colleague of Grandpa, and on their latest expedition together he disappeared. Now Yugi knows just where Grandpa had gone, but the Pharaoh still suspects something. They just happen to win a trip; their plane just happens to crash; and they just happen to meet the man who was the last person to see Grandpa. It all seems a little bit coincidental. Brisbane shows Yugi and the gang where he last saw Solomon. Yugi and his friends are surprised when they discover that Brisbane last saw Solomon in a pyramid.
Brisbane explains that he believes it to be the legendary pyramid of Alexander the Great, and that it's supposed to contain some sort of ancient game. They check it out, narrowly avoiding a number of dangerous traps, and come across a room that, as Tristan put it, is the size of Cleveland. The floor looks like a giant map of different land types, which looks incredibly familiar to Yugi. Joey decides to check it out but, to everyone's surprise, disappears into thin air the second he steps on the map. Coming to the conclusion that Solomon must have gone to the same place as Joey, the rest of the gang decide to follow, leaving a bewildered Brisbane behind.
They find themselves in a forest, with Joey nowhere to be seen. Yugi notices a lot of egg-shaped rocks around, but before they can investigate, some giant cockroaches ("Gokibore"), and a giant praying mantis ("Kamakiriman") ambush them. Yugi, Tristan an Téa escape, but are split up in the process.
Yugi is cornered by the mantis, so the Pharaoh takes over to protect him. He accidentally touches one of the strange egg-shaped rocks whilst jumping, which somehow causes "Celtic Guardian" to appear. "Celtic Guardian" attacks the mantis, destroying it.
Back in the forest, "Celtic Guardian" disappears in a beam of light, transforming into a small capsule. Now, Yugi knows where he'd seen this before.
The heroes have to discover the secret of the Capsule Monsters world, and figure out how to escape the island. In addition, someone in the real world may desire to use the power of the Capsule Monsters for his own evil plans.
Two weeks after Yugi's battle with Kaiba in Death-T, Yugi gets a call from Kaiba, who tells him to meet for game of Duel Monsters at the top floor of KaibaCorp. Yugi accepts, and when the Duel begins, they use a special variation called the "Bingo Rule," which prevents the used of a specific card in each player's Deck. Kaiba seems to be himself, but plays a different trump card, the "Automatic Giant".
Mokuba stumbles in on them, and tells Dark Yugi that Kaiba has not yet awoken from his catatonic state. It turns out that the Kaiba that Yugi is playing against is a Cyber Kaiba, controlled by the KaibaCorp computer, and using all of Kaiba's memories.
Dark Yugi defeats the "Automatic Giant" and Kaiba with a card called "The Unknown Egg", restoring everything to normal.