Duelist Kingdom

In the manga, the story begins with Maximillion Pegasus. Yugi Mutou's defeat of Seto Kaiba (in the manga, the defeat occurs at Death-T in the previous story arc, while in the anime, this occurs during the story arc) brings him to the eye of Pegasus. Pegasus seeks to reacquire his deceased love, but to do that, he needed Kaiba's holographic technology. Forced by the Big 5 of Kaiba Corporation to defeat Yugi before being able to take over KC, Pegasus traps the soul of Solomon Muto, Yugi's grandfather, forcing Yugi to join the Duelist Kingdom tournament. In the manga, Kaiba emerges from a coma after Pegasus announces the tournament. In the anime, Kaiba is still shocked at Yugi's upset, and refrains from joining and goes to his retreat. Kaiba's arrogance urges him to regain his previous title, but it also causes him to drop out of the tournament.

Pegasus had selected only the best for his Duelist Kingdom tournament. That means that Joey Wheeler would not be included. However, Jonouchi needs the $3,000,000 to pay for an eye surgery for Serenity Wheeler that would prevent her from going blind. Therefore, Yugi lends one of his star chips to Jonouchi, and they start dueling their way to the top. Pegasus gives each duelist two star chips, and the first four to get ten would be the finalists.

Duel with Seto Kaiba
In the anime, the arc begins with the story began with Yugi's duel with Seto Kaiba, a genius programmer and business sensation. Kaiba is the greatest duelist in the world, and was the favorite to win the most recent duel monsters tournament. Naturally, Kaiba's genius, glory, and business skills make him very arrogant. Kaiba also had an obsession with the Blue-Eyes White Dragons, and is spending great effort to gain all four of them. He already has three, and is searching for the fourth. Kaiba finds the fourth one in Yugi's Grandfather's game shop (The Kame Game Shop in the manga and Japanese versions). Kaiba failed to buy or trade for it, so he forced Yugi's Grandfather into a duel, with Kaiba as the victor. Then, Kaiba tears up the last Blue Eyes, because in the game, a person cannot have more than three of the same card (The reason for this is different in the manga's story). Next, Yugi duels Kaiba, and upsets the world champion. This story in the Duel Monsters anime is derived from several manga chapters.

Kingdom Duels
Yugi and Jonouchi's path to the finals:


 * Yugi defeats Weevil Underwood, the Japan/Duel Monsters tournament Champion. Has three chips because he wagered his deck in exchange for another star chip.
 * Mai defeats random duelist. Has 3 star chips.
 * Jonouchi defeats Mai Valentine. Has two star chips.
 * Yugi defeats Mako Tsunami, a sea duelist. Has five star chips.
 * Yugi loses two star chips after Mokuba Kaiba steals them and then Kimo, Pegasus's main bodyguard, throws them into the ocean.
 * Yugi defeats the Player Eliminator ("Dark Kaiba" also known as "Yami Kaiba" in the dub) Has six star chips.
 * Jonouchi defeats Rex Raptor, the Japan Tournament Runner-up. Has four star chips and Ryuzaki's Red-Eyes Black Dragon card as part of the ante.
 * In the anime version, at night, Yugi beats Dark Bakura in a shadow game. This duel was adapted from the Monster World RPG game in Volumes 6 and 7 of the Yu-Gi-Oh! manga and it does not happen in the manga.
 * Mai gets beaten by Panik loses 8 star chips.
 * Yugi beats Panik to give Mai back her star chips that she lost.
 * Jonouchi beats Bonz, a zombie duelist with cards from Bandit Keith. Has 8 star chips.
 * Jonouchi and Yugi fight together against Para and Dox, who are player eliminators. Both have 10 star chips.
 * However, Pegasus also has to get Kaiba's technology. Pegasus appeals to the Big 5, Kaiba's vice presidents, and abducts Mokuba. Kaiba goes to Duelist Kingdom to get Mokuba back. Pegasus traps Mokuba's soul in a card.
 * In the English anime, Pegasus sends Mokuba to the Shadow Realm and forces Kaiba to beat Yugi to try to get Mokuba back. The Big 5 are fired after this arc in the manga.
 * Kaiba confronts Yugi on the top of the castle, explaining his situation to him, and begins their duel. Kaiba merged his three Blue-Eyes White Dragons to make Blue-Eyes Ultimate Dragon. However, his combo was destroyed with an inpenetrable wall of Kuriboh, Mammoth Graveyard, Living Arrow, and Polymerization. Only when Kaiba threatened with suicide if he would lose, Yugi overcame his other self and surrenderd. Yugi was so shaken up by this experience that he broke down in tears and vowed never to duel again for fear that his other self could cause someone serious harm.
 * In the Anime, to get Yugi back into the finals, Téa Gardner decides to duel Mai Kujaku who has ten star chips and another eight to repay Yugi for his duel with Panik. However, Mai did not want to give it seeing Yugi's dejection. Although Mai could have won with the card "Harpie's Feather Duster", she instead forfeits to Anzu. Yugi, inspired by Anzu's dedication, receives the boost he needed to galvinize himself for the finals.
 * In the manga, Mai simply gives the star chips to Yugi, rather than dueling Anzu for them.

The Finals

 * Before the finals, Pegasus introduces Kaiba to the finalists, and the two duel. If Pegasus wins, he takes Kaiba's soul; if Kaiba wins, he gets Mokuba back. Althought Kaiba fought bravely using his Crush Card combo, Pegasus' Millennium Eye reads his mind. At the end, Pegasus uses Doppelganger to copy Kaiba's Crush Card Virus, and wins the duel.
 * First Duel of the finals comes to Mai and Yugi.
 * In the English anime, Yugi tries to hold back Yami Yugi's dueling strength because of his willingness to beat Kaiba even if it meant his death. However, in the manga, Yugi is concentrating on the coming duel with Pegasus and not on the duel with Mai.
 * In both cases this leads to Yugi making mistakes. Because of these mistakes, Mai gets a huge advantage, with the Harpie Lady Sisters and Harpie's Pet Dragon. However, she eventually forfeits when Yugi summons "Black Luster Soldier" to the field.
 * Next, is Jonouchi against "Bandit" Keith Howard.
 * Bandit Keith steals Jonouchi's entry card, nearly causing Jonouchi to be disqualified. However, Jonouchi uses Mai's entry card to play. Even though Keith cheats, he still loses. Then, Pegasus confronts Keith and says that he saw his cheating, whereupon Keith tries to get the prize money by force.
 * In the anime, Pegasus drops Keith down a trap door, and Keith eventually reappears prior to Battle City under the mind control of Marik Ishtar. In the manga, Pegasus inflicts a penalty game on Keith, causing his apparent death.
 * Last, it is the duel between Jonouchi and Yugi, which is only in the anime. They stay rather even, but Jonouchi gains a good lead. Ultimately, Joey loses due to a miscaculation on his part. He thought that "Time Wizard" would weaken "Dark Magician", instead it turned it into Dark Sage. Yugi, after telling Jonouchi that this attack is the toughest he has ever made, attacks him and wins the duel.

Match of the Millennium

 * Pegasus applies the same strategy to Yugi as he did to Kaiba. He's able to play Toon World, making all his monsters invincible. Pegasus saw every one of Yugi's strategies, and counters every one of them. However, Yugi then uses mind shuffle. Yugi and Dark Yugi keep changing places, and Pegasus cannot see the mind of the other. Therefore, he does not know what Yugi plans.
 * In the English anime, Pegasus then sends the duel into the Shadow Realm, where his illusion monsters come into play. In the manga and Japanese anime, Pegasus does not use the Shadow Realm as the Shadow Realm does not exist in either of those versions.
 * Ultimately, Yugi wins.

Aftermath

 * In the end of it all, Pegasus's Millennium Eye gets stolen by Dark Bakura, and the souls of Mokuba Kaiba, Seto Kaiba and Sugoroku Mutou are restored. Yugi gives Jonouchi the money for the eye surgery of Jonouchi's sister.