This series starts with Yugi teaching Jonouchi how to play Duel Monsters. He talks about his grandpa’s shop, and Seto Kaiba overhears. Everyone goes to the Kame game shop, and Sugoroku brings out his most cherished card, Blue-Eyes White Dragon. There are only 4 in existence. Kaiba walks in a sees the Blue-Eyes White Dragon. He offers a briefcase full of rare cards for it, but Sugoroku won’t give it up because it was given to him by a special friend. Later, Kaiba sends some men to abduct Sugoroku, and forces him to duel for the Blue-Eyes. He loses, and gets tossed out, right as Yugi and gang arrive. Kaiba steps out and rips the Blue-Eyes in half. Yugi challenges Kaiba to a duel, and it’s revealed that Kaiba has the other 3 Blue-Eyes White Dragons. Yugi is about to give up, when he remembers his friends, and keeps going. He collects the 5 pieces of Exodia in his hand, and wins. He then banishes the evil in Kaiba’s mind.
The next day, Yugi receives a package from Industrial Illusions, that includes an invitation to the Duelist Kingdom tournament, and a video tape introducing Pegasus J. Crawford, the creator of Duel Monsters. Pegasus takes Yugi to the shadow realm to duel, and the souls of Jonouchi, Honda, Anzu, and Sugoroku. Yugi loses, and Pegasus puts Sugoroku’s soul in a blank Duel Monsters Card. Yugi enters the tournament to get his grandpa’s soul back. Each guest receives a dueling glove and 2 star chips. Jonouchi needs money for his sister’s, Shizuka, eye operation, so Yugi gives him a star chip so he can enter and try to win the cash prize.
On the boat to Duelist Kingdom, Jonouchi buys a pack of Duel Monsters that includes Shield and Sword, Baby Dragon, Kunai with Chain, and Salamandra. Yugi gives Jonouchi Time Wizard to combo with his cards. They meet Insector Haga, the Japan national champion. He takes Yugi’s Exodia and throws them into the ocean. Jonouchi jumps in and tries to save them, but he can’t. This is another reference to how friendship bonds duelists together. On the island, the first duel Yugi has is against Insector Haga. Since Yugi only has 1 star chip, he antes his deck as well against 2 of Haga’s chips. Yugi defeats Haga, and Jonouchi takes his dueling glove. Another good duelist, Mai Kujaku, challenges Jonouchi for an easy win, but using the cards he got on the boat, Jonouchi defeats Mai. The next day, everyone realizes they didn’t bring food along, and instead of eating berries as Honda suggested, Jonouchi smells fish and they run off to find roasting fish over a fire. Ryouta Kajiki jumps up and challenges Yugi to a duel. Yugi beats Kajiki after a hard duel.
Pegasus sends some henchmen to kill Kaiba, but he grabs what he’s working on and jumps out the window. Yugi runs into Kaiba’s brother, Mokuba who escaped from Pegasus’ castle. He runs off with Yugi’s cards, and gets caught by guards. The only way to get Mokuba back is to duel the “ghost of Seto Kaiba”. It’s later revealed that it’s a Player Killer in a costume. The real Kaiba is underground, uploading viruses to help Yugi. Yugi wins, but Mokuba is still taken away. Yugi grabs Kaiba’s deck.
Upset about her loss, Mai tries to find a way to get back at Jonouchi. Ryuzaki, Runner-up in the Japan national tournament, challenges Mai because she tricked him out of his fancy room on the boat. During the duel, Ryuzaki summons the Red-Eyes Black Dragon, one of the most powerful dragons at the time, and Jonouchi has Time Wizard on the field. Jonouchi proposes they ante the cards they have on the field as well as Star Chips. He activated Time Wizard, and defeats Ryuzaki. That night, the gang is visited by a classmate, Ryou Bakura. He gets everyone to identify with a card. This is where we first see Yugi’s relationship to Dark Magician. The spirit in his Millennium Ring takes over, and takes them to the Shadow Realm. Everyone’s souls are transported to Yugi’s deck. As Bakura reaches for the Millennium Puzzle, Yami Yugi appears and challenges Bakura to a duel. In this duel, when Yugi plays the cards his friends identified with, their souls come out on the field. This is where everyone realizes Yugi and Yami Yugi are different. Bakura helps Yami Yugi defeat Yami Bakura, and everyone’s souls are returned.
After the duel with Bakura, there was a scream that turned out to be Mai losing to Player Killer. She lost all her star chips, and Yugi challenges P.K. to get them back. Yugi beats P.K. and uses Mind Crush. Mai doesn’t accept the star chips at first, but when Jonouchi grabs them, she gets mad and takes them. Later on, Kaiba arrives and Yugi gives him his deck. Jonouchi challenges Kaiba to a duel, and loses miserably. This is the first time we see the Duel Disk in action. The next day, Jonouchi gets knocked out by Bandit Keith’s men. He gets dragged into a cave and is forced to duel Ghost Kotsuzuka. Yugi and gang arrive, and Jonouchi ends up winning with Shield and Sword. Keith and his men seal the entrance to the tunnel, and he takes Kotsuzuka’s star chips.
Kaiba enters a secret entrance to Pegasus’s castle to find Mokuba in a jail cell. Pegasus comes along and puts Mokuba’s soul in a blank card. He tells Kaiba he will duel for Mokuba’s soul if he defeats Yugi. After tripping a couple traps, Yugi and gang realize the tunnel is man-made. Bakura’s Millennium Ring points to the direction of another Millennium Item, and it leads them to a room with a dueling arena. Player Killers, Mei and Kyuu jump out and challenge Yugi to a team duel. Yugi and Jonouchi accept. To get out of the maze, they must beat Mei and Kyuu and choose a door. Yugi and Jonouchi defeat Mei and Kyuu’s Gate Guardian and escape to find Kaiba at the entrance of Pegasus’s castle. Kaiba challenges Yugi to a duel because Kaiba can’t get into the castle without star chips. Kaiba summons Blue-Eyes Ultimate Dragon, but Yugi finds a way to defeat it. Unwilling to lose, Kaiba threatens to jump off the castle if Yugi attacks for the win. Yami Yugi starts to attack, but little Yugi breaks through and stops it. Kaiba attacks and takes Yugi’s star chips. Mai comes along and tries to give Yugi star chips, but he is too sad and scared to take them. Anzu challenges Mai for the chips and after realizing Anzu’s actually a strong duelist, Mai gives up before she would win.
Inside, Kaiba tries to make Pegasus use the duel disk, but the only way he will is if Mokuba’s lifeless body uses it for him, so they use the duel arena. Kaiba can do nothing against Pegasus’s toon monsters. Pegasus puts Kaiba’s soul into a card. Later on, everyone gets their opponent for the finals; Mai vs. Yugi and Bandit Keith vs. Jonouchi. That night, Yugi hears his grandpa’s voice calling him. He goes outside to find 3 crosses. One has his grandpa’s card on it, and the other two have Kaiba’s and Mokuba’s. Meanwhile, Honda, Anzu, and Bakura try to find out how Pegasus knew what cards Kaiba had in his hand. They go into a tower to find a room full of paintings of Cecilia, Pegasus’s dead wife. Pegasus uses his shadow power to take them to Ancient Egypt where a shadow game is being played. He is about to kill them when Yami Bakura appears and takes them back to reality where they don’t remember what happened. Keith sneaks into Jonouchi’s room and steals his entry card to the finals.
During the first match of the finals, Yugi starts losing to Mai because he is afraid to let Yami take over. After Mai tells him to duel his best, he lets Yami come out and he wins by summoning Chaos Soldier (Black Luster Soldier). Jonouchi can’t find his card, so Mai gives hers to him. Keith is obviously confused when Jonouchi has one, and Pegasus notices. Through the duel, Keith cheats, but Jonouchi still wins. Pegasus tells everyone he cheated and has him dragged off. Keith comes running back and puts a gun to Pegasus’s head, but he pushes a button and Keith falls to the ocean. Final match: Yugi vs. Jonouchi. After a good duel, Yugi wins and starts against Pegasus. Using his Millennium Eye, Pegasus knows every card Yugi draws. During this duel, Yami Bakura takes over and runs off to find Mokuba’s body. After a while, Honda chases after him. Bakura gets Mokuba and is chased by guards. When Bakura and Honda are chased to an open window, Bakura uses the Millennium Ring to bring Man-Eater Bug to life and it eats the guards. Honda knocks Bakura out and throws the Millennium Ring into the forest. Back at the duel, Yugi remembers his grandpa telling him to trust in the puzzle, not the spirit inside. After each turn, Yugi and Yami switch minds. They call this “Mind Shuffle”. Since Pegasus can’t read Yugi’s cards anymore, he takes them to the shadow realm, where little Yugi can’t stand the pressure. Later on, the power of Yugi’s friends keeps Pegasus from reading his mind. Yugi summons Magician of Black Chaos and wins the duel.
Pegasus runs upstairs to the room full of Cecilia paintings, and explains why he wanted Kaiba Corp. He was going to try to merge the power of the Millennium Items with the technology of Kaiba Corp. to revive Cecilia. Bakura steps in and challenges Pegasus to a shadow game. Bakura wins and rips Pegasus’s Millennium eye out. Shadi appears and enters Yugi’s mind. He finds out Yugi has two memory chambers and realizes Yugi was meant to have the puzzle.
Everyone goes back to Domino Town, and Yugi is challenged by a little girl named Rebecca. She’s the genius American champion of Duel Monsters. She says Sugoroku stole the Blue-Eyes White Dragon from her grandpa, but when they give here the ripped Blue-Eyes she gets mad. She duels little Yugi, and Yugi forfeits. She doesn’t care about her monsters, and purposely destroys them to feed Shadow Ghoul. Sugoroku finds out Rebecca’s grandpa is Arthur Hopkins, his old friend from the Egyptian excavations. They discovered Duel Monsters originated in Egypt. They were trapped underground, and dueled for the last bit of water. Sugoroku gave up, just as Yugi did against Rebecca. Later, Kaiba fires the Big 5, Kaiba’s KC employees, for conspiring with Pegasus. They tell Kaiba his virtual reality game, Duel Monster Quest is finished, and he wants to try it out. It is a trick. The Big 5 changed the game to get Kaiba trapped inside. Mokuba escapes and gets Yugi and gang to help free Kaiba. Yugi, Jonouchi, and Mokuba enter the game and save Kaiba. This is where we first see Five God Dragon and Master Dragon Knight.
A new transfer student arrives in school named Ryuuji Otogi. He starts a game store that attracts business away from the Kame shop. The shop specializes in Dungeon Dice Monsters, a game Otogi invented. Jonouchi loses to him in a duel, and is forced to wear a dog suit and become Otogi’s slave. Yugi challenges Otogi to get Jonouchi back, but Otogi only accepts if it’s a game of DDM. This game is televised, and if Yugi loses, he can never play Duel Monsters again. Otogi blames Yugi for not being able to get in touch with Pegasus to finalize a DDM manufacturing deal. Otogi doesn’t tell Yugi the rules, but after a losing game, Yugi comes from behind and wins. It was Dark Magician that helped Yugi win, and Pegasus was the one who suggested Dark Magician be included in DDM.