Yugi Muto, known as Yugi Mutou in the Japanese versions, is the main character and protagonist of the original Yu-Gi-Oh! series, along with Yami Yugi. Yugi is kind-hearted and child-like. He is good at games, riddles, and puzzles, especially Duel Monsters.
Yugi possesses the Millennium Puzzle, which allows his body to bear host to the spirit of the Puzzle, Yami Yugi. Yugi was initially unaware of his existence and control of Yugi's body would involuntarily shift to Yami, when Yugi or his friends are wronged.
Yugi is part of a close-knit group of friends: Joey Wheeler, Tristan Taylor, and Téa Gardner as well as Ryo Bakura and (In some cases) Mokuba Kaiba. Miho Nosaka is also one of Yugi's friends in the first series anime. Yugi's friends often cheer him on from the sidelines, and Joey has dueled at his side. Yugi has been friends with Téa since childhood and has a crush on her. Téa has been shown to have feelings for both Yugi and Yami Yugi.
In Japanese, the first characters of "Yūgi" and "Jōnouchi" combine to form "Yūjō" (友情), which means "friendship". The "Yu-Jo Friendship" card is named after the word and the fellowship between the characters.
Yugi's character design was overseen by Kazuki Takahashi. His normal outfit consists of the standard male Domino Junior/Senior High uniform complete with a closed buckled collar. His extremely extravagant hair features multiple layers including long blond crooked, pointy locks for his fringe, the rest features a set of five large spikes and two smaller spikes colored black with a magenta sheen along the edges. So far, he is the only character in the franchise to have his hair divided into three colors. He wears the Millennium Puzzle on a lace around his neck. In the manga and second series anime, the lace is later replaced with a chain. In the manga (post Volume 7) and in the second series anime, he often wears a KaibaCorp Duel Disk on his left arm.
When he plays Dungeon Dice Monsters against Duke Devlin, he wears a black long-sleeves shirt, a gray sleeve-less vest, dark blue pants and black shoes.
When he and Téa took a day together to find out about the Millennium Puzzle, he wore a black linen shirt and several pieces of wrist-chains, along with a pair of leather pants.
In Yu-Gi-Oh! GX, Yugi is shown much taller, as he is taller than Jaden who is taller than Yugi's past self. In Yu-Gi-Oh! GX, Yugi's present day face is not directly shown. However his voice now resembles Atem's as he is now older. It is possible that he now looks like Atem.
In Yu-Gi-Oh! Capsule Monsters, Yugi wears a different attire of a violet jacket and jeans. He also wears the Capsule Shooter on his left arm. In episode 4, he gains a duel armor that allows him to become one with one of his capsule monsters.
The voices differ slightly between the different series and the English dub, although commonly the voice of Dark Yugi is stronger and more confident than that of Yugi.
In the first series anime, Yugi and Dark Yugi are voiced by Megumi Ogata. Yugi's voice is positively timid, rarely showing any strength and almost always being polite in his speech, using honorifics and "boku" as his personal pronoun. Dark Yugi's voice is much rougher, uses "ore" as his personal pronoun and rarely ever uses honorifics. He also has a catchphrase, "Saa, geimu no jikan da!", which means "Come, it's game time!" or "Come, it's time to play a game!"
In the Japanese version of the second series anime, Yugi and Dark Yugi are voiced by Japanese singer Shunsuke Kazama. Yugi has considerably more confidence than in his previous appearance, but is still very polite. It's harder to distinguish between his voice and Dark Yugi's, but Dark Yugi's tone is considerably sterner and has the same pattern of speech as his previous appearance. This series also established Yugi calling Dark Yugi mou hitori no boku (the other me) and Dark Yugi referring to Yugi as aibou (partner).
In the English version of the second series anime, Yugi and Yami Yugi are voiced by Dan Green. Yugi's voice is high pitched and sometimes strained in more emotional moments, and generally has a friendly tone towards everyone. Yami Yugi's voice, in comparison, is fierce and commanding. Yugi's last name is pronounced "Mohtoh" in this version, although it is still spelled "Muto". In the Singaporean dub of the second series anime, Yugi and Yami Yugi are voiced by Chuck Powers. In this dub, Yugi's voice is soft and slightly high-pitched, while Yami Yugi's voice is near the total opposite. In the Singaporean dub, both Yugi and Yami Yugi speak with a slight drawl. In the first season, Yugi calls Yami Yugi "Spirit", then in other seasons Yugi started to call him "Pharaoh". Sometimes, he also calls him Yami. Yami Yugi always called Yugi by his name.
Joey and Tristan used to bully Yugi. Joey even went as far as taking a piece of Yugi's Millennium Puzzle and throwing it into a canal. However Yugi stood-up for Joey and Tristan, when they were attacked by Ushio, claiming that they were his friends, whereas Ushio claimed he was protecting Yugi in order to earn money. Joey and Tristan came to be Yugi's friends after the incident and Joey recovered the piece of the Puzzle.
After solving the Millennium Puzzle, Yugi unknowingly became host to Yami Yugi, the spirit of Pharaoh Atem. He shared his body with Yami, who occasionally takes control, typically to help Yugi and his friends.
Yugi and Joey once visited Burgerpalooza, only to find Téa working there. She feared that if they told, she would get expelled as it's against school rules to have part-time jobs. (In the English version, she worried about getting fired, as they could have revealed that she was under 18, the required age to work there.) She splattered their burgers in ketchup, warning them not to tell. They told her that they did not even know she worked there, and they wouldn't say a word.
Yugi later found Téa in a warehouse, being filmed by a pervert, who threatened to reveal she was working at Burgerpalooza. (In the English version, he was a mugger who tricked her by writing a note, pretending Yugi and Joey had given her a dance studio.) Yugi tackled the man, but got thrown against a wall. Téa was also knocked unconscious after trying to attack him. Yugi then transformed into Yami Yugi, who defeated the man in a card draw game and Mind Crushed him. Yugi came to believe that he had saved Téa himself, although he didn't remember how he did it.
Yugi defeated Joey in Duel Monsters at school and decided to invite Joey, Téa and Tristan to see his Grandpa's rare card, the "Blue-Eyes White Dragon", after school. Seto Kaiba, who overheard, kidnapping Grandpa and forced him into a Duel for his "Blue-Eyes", as he refused to trade or sell it. Yugi and his friends caught up after Solomon had already been defeated, and witnessed Kaiba tear-up the "Blue-Eyes White Dragon" in front of them. Outraged, Yugi challenged Kaiba to a Duel, and Solomon gave Yugi his Deck. Yugi dueled Kaiba as Yami Yugi and discovered Kaiba had the other three "Blue-Eyes White Dragons" in his Deck but defeated him using "Exodia the Forbidden One", taking Kaiba's title as the Duel Monsters World Champion.
Since Joey had been having trouble with winning in Duel Monsters, Yugi asked his grandfather to help train Joey.
Maximillion Pegasus heard of Yugi's victory over Kaiba and sent him a videotape inviting him to participate in his Duelist Kingdom tournament. Pegasus appeared on the TV and dueled Yugi on the spot, while freezing everyone else in the room. Pegasus placed a time limit on the Duel and won because time ran out seconds before Yugi could claim victory. As a penalty for Yugi's defeat Pegasus stole Grandpa's soul.
On the ship, Yugi met Weevil Underwood, who acted friendly towards him and told Yugi that he knew of secret new rules to be introduced in the tournament. Shortly after Weevil left, Yugi gave Joey the "Time Wizard" card, telling him how it can be helpful in a tight spot. Yugi met Weevil again later and showed him his "Exodia" cards, which Weevil tossed overboard, to hinder Yugi's Deck. Joey jumped into the water to recover them, but after getting two of them was hit by the current and Yugi dove in to save him. Both of them were then rescued by the stowaways; Téa and Tristan, who threw them a rope ladder.
Once the tournament started, Yugi tracked down Weevil to get revenge, but Weevil fled, leading him into a forest. Yugi suspected this was to do with the new rules Weevil mentioned. Weevil led them to a meadow, where he accepted Yugi's challenge, as his monsters got Field Power Bonuses there. Yugi switched to Yami Yugi, who bet both his Deck and Star Chip, earning him Weevil's two Star Chips after he won.
While searching for food, Yugi and his friends, found fish Mako Tsunami had prepared. Unbeknownst to them, Mako had set it as bait to lure opponents, to where his monsters greatly benefit from the field. Mako then appeared, angered over them stealing his food. After Yugi introduced himself, Mako was happy to meet the duelists, who defeated Kaiba and shared the food with them. Yugi got up to leave, but Mako stopped him by throwing a harpoon in front of him and demanded a Duel. Yugi switched to Yami and defeated Mako, winning two more Star Chips.
Yugi and his friends saw a contestant, being forced to leave the island as he was out of Star Chips. The boy claimed they had been stolen, along with his Deck. He described the thief and where he met him. Yugi promised to get his Star Chips back, before the boat left the island. Back at the scene of the crime, they met the thief, who was Mokuba Kaiba with his face disguised. He dueled Yugi with five Star Chips on the line and Yami Yugi soon realized that he was Mokuba. Mokuba explained how Yugi humiliated his brother, causing him to leave, giving Pegasus an opportunity to take over KaibaCorp. Mokuba sought revenge on Yugi for this. Unable to win the Duel, he made a grab for Yugi's Star Chips, but Yami discouraged Mokuba and promised to help him and Seto.
The group made their way back to the bay, but the boat had already left. Mokuba showed Kemo that Yugi won back the Star Chips, but Kemo slapped them into the water, including some of Yugi's. Kemo grabbed Mokuba to take him back to Pegasus, but Yugi challenged Kemo to a Duel for Mokuba's freedom. Since Kemo wasn't a duelist, he told Yugi to come back in an hour (4 hours in the English version) and he'll have an opponent arranged for him.
Yugi returned to the spot and faced Ghost Kaiba, who pretended to be the actual Seto Kaiba and used his Deck. With the help of the real Kaiba, who weakened Ghost Kaiba's "Blue-Eyes White Dragons", via a virus, Yami Yugi won. Yugi retrieved Kaiba's Deck, but Kemo had already disappeared with Mokuba.
Yugi was not allowed to help Joey in his Duel with Rex Raptor. As the Duel started Yugi went to find Tristan, who left in a huff with Joey for accepting those conditions. Tristan reminded Yugi that he should still be at the Duel to offer Joey his friendship, so the two of them returned to watch.
That night, Mai shared her food with Yugi and his friends, although she promised that they would be enemies again tomorrow.
Ryo Bakura appeared at their campsite, shortly after Mai left for a walk. While the group talked about cards they own, that they an identify with, Yugi encouraged Téa to pick one for herself. Yugi picked the "Dark Magician" as his. After everyone had exchanged, which cards they recognize with, Bakura suggested that they play a friendly Duel, where Yugi includes the cards Joey, Tristan and Téa choose; "Flame Swordsman", "Cyber Commander" and "Magician of Faith" in his Deck and he can show them how his card, "Change of Heart" works. Bakura changed to Yami Bakura, who trapped the group's souls in the cards they selected. He proceeded to take Yugi's Millennium Puzzle, but Yami Yugi emerged. Yami faced Yami Bakura, in a Shadow Game, to return his friends, but staking his Millennium Puzzle.
Yugi's friends appeared in place of the monsters they selected as Yami Yugi Summoned them. When the "Dark Magician", Yugi was Summoned, the two Yugis met. In the Japanese version, Yugi was aware of Yami's existence and the two of them agreed now is not the time to keep secrets. In the English verion, Yugi was unaware of Yami's existence until that time, though he said he often heard a powerful voice coming from the Millenium Puzzle. Yugi told his friends of Yami's existence, that he is the spirit of the Millennium Puzzle and apologized for not telling them before. In the English version, Yugi admitted to having felt Yami's presence while he dueled and felt they could trust him. Yami managed to win the Duel, with the help of Ryo betraying Yami Bakura, returning everyone to normal. Although Téa, Tristan and Joey believed the Duel to have been a dream. Yugi didn't take time to explain as they heard Mai scream.
The group found the Eliminator, PaniK, who had just beaten Mai and taken all eight of her Star Chips. Yugi accused PaniK of being a coward and dueled him as Yami Yugi, winning back Mai's Star Chips. He offered them to Mai, who reluctantly took them back, remarking that she owed him one.
Later that night Kaiba arrived on the island and Yugi returned his Deck.
The next day, Mai left a letter explaining she had left and owes Yugi for winning back her Star Chips. Joey later got separated from his friends, who searched a cave after finding his wallet outside. After running from many traps, they found Joey in a Duel with Bonz. Joey won, but Bandit Keith's gang trapped Yugi and his friends in the cave, by sealing the entrance with a boulder.
Using Bakura's Millennium Ring as a guide, the friends found the Paradox Brothers guarding an exit. Yugi and Joey faced them in a Tag Duel to gain passage. After winning Yugi and Joey, each had enough Star Chips to enter the finals and Yami Yugi passed the brothers riddle test in order to exit.
At the stairs to Pegasus' castle, Téa pondered on Yugi's differing personalities and wondered if there could be two Yugis. Yugi admitted to feeling as though there is someone else living inside him, but hoped he wasn't going crazy.
At the top of the stairs, Kaiba blocked the way and talked Yugi into a Duel. Yami took control and faced Kaiba, using his Duel Disk technology. As Yami was about to win, Kaiba stood up on the edge of the castle, such that the shockwaves from Yugi's attack may cause him to fall to his death. (In the English anime, Yugi spoke to Yami, telling him not to do it.) Yami contemplated, but in the end decided to attack. Téa ran to Yugi insisting that this isn't like him and calls for the ordinary Yugi to come out. Yugi took control in time to cancel the move. He fell to his knees, horrified by what he'd almost done. Kaiba took his turn and won the Duel, claiming five of Yugi's Star Chips.
Now fully aware of the other Yugi's existence, Yugi admitted it to his friends, telling them that he is afraid of him and consequently afraid to Duel. Kaiba called Yugi weak, but Téa protested arguing that Yugi saved him and Kaiba is the real loser. After Kaiba left, Yugi continued to mope. Joey offered Yugi to take his Star Chips, so he may enter the finals, but Yugi ignored him. Frustrated Joey grabbed Yugi by the shirt, asking him if he cares about his Grandfather.
Mai appeared and was briefed in on what just happened. She offered Yugi her excessive Star Chips, as per her promise from earlier, but Yugi didn't even acknowledge Mai's appearance. Annoyed Mai told him to grow up and hang on to the Star Chips. She accused him of being afraid to Duel again and challenged him. Téa instead accepted the Duel, to win back Yugi's Star Chips.
Yugi began to slowly snap out of his depression as he watched Téa duel. After Mai surrendered, Yugi approached her about the face-down card she didn't use. Mai denied that she lost for him. (In the English version, she said that some cards just aren't worth playing.)
Inside the castle, the group were invited to watch Pegasus duel Kaiba. Seeing as Kaiba was dueling to save Mokuba, Yugi opted support to Kaiba. Kaiba was trapped in Pegasus' "Soul Prison" card, after his defeat. Yugi then shouted down to Pegasus' asking who he is to mess with people and their families like this.
The finalists along with Téa, Tristan and Bakura were treated to a meal that evening, where the finalists got paired-up. After the meal, Yugi gave Joey his "The Glory of the King's Hand", as it is mandatory for each finalist to possess either it or "The Glory of the King's Opposite Hand".
That night, Yugi was woken by his grandfather's voice, calling him. He followed it and found a "Soul Prison" card, with his grandfather's soul inside. Solomon warned him about Pegasus and is accompanied by the cards containing Seto and Mokuba Kaiba's souls. Yugi woke up afterwards, wondering if it was a dream.
Yugi faced Mai in the first Duel of the finals. Yami Yugi gives little effort to the Duel, as he worried about facing Pegasus. (In the English version, Yugi refused to let Yami duel, fearing how he may harm their opponent.) This resulted in Yugi playing poorly. Encouraging words from Mai returned the Yugis to the top of their game and allowed them to turn the Duel around and emerge with a win.
Yugi faced Joey in the final round. Joey used all he learned from Yugi, but was still defeated by Yami Yugi. Afterwards Joey offered to give "The Glory of the King's Hand" back to Yugi, so he may claim the prize money. However Yugi declined, as he had entered to tournament with the intent of saving his grandfather and now the Kaiba brothers. The money was not important to him, but Joey needed it for his sister's eye operation.
Yugi advanced to duel Pegasus. At the start of the Duel, Yugi requested that the Kaiba brothers' souls be released as well as his grandfather's, if he wins. Pegasus accepted but indicated that he plans on taking Yugi's soul if he wins. Pegasus used his Millennium Eye to read Yami Yugi's mind during the Duel, but Yugi had an idea about countering Pegasus's powers by the risky strategy of having him and Yami switch minds each time they played a face-down card, thus preventing Pegasus from reading their strategy while running the risk that one of them would attempt something that would hinder the other's plans. After the Yugis destroyed Pegasus' "Toon World" card, Pegasus transported them all into the Shadow Realm. In the Shadow Realm, Yugi lost his life energy while doing the mind shuffle strategy, lacking the spiritual strength to play on that level, and Pegasus continued successfully reading Yami's mind until Joey, Téa, and Tristan blocked his Millenium Eye. Yami defeats Pegasus, returning them both back from the Shadow Realm.
Pegasus disappeared after his Duel with Yugi. Determined to ensure the captive souls are returned, Yugi and his friends searched for Pegasus. They found a number of Pegasus' men carrying him away after he was assaulted by Yami Bakura. Croquet explained that he was attacked. (In the English version, he said that Pegasus had fallen ill.) Yugi and company headed to Pegasus' tower, where they found a diary entry addressed to new King of Duelists who defeats him, explaining why he created Duel Monsters. Yugi then spotted the three "Soul Prison" cards, which are now blank, meaning the souls are no longer imprisoned.
As he left the tower, Yugi bumped into Shadi, who used his Millennium Key to enter Yugi's mind. To Shadi's surprise he found two soul rooms; one for Yugi and one for Yami. Shadi wound up in a Shadow Game with Yami, but was rescued by Yugi. Yugi informed Shadi that he doesn't believe his other self intends to harm him and asked Yami to release Shadi from the game.
A door opened, leading them to a room lined with stone tablets of Duel Monsters. Yugi learned from Shadi that millennia ago, Egyptian kings played Shadow Games with real monsters and magic. After the games became a war that threatened to destroy the world, one brave pharaoh sealed the magic away. The duo were confronted by the Dark Magician. Shadi prepared to counter by Summoning the Blue-Eyes White Dragon. However Yugi insisted that the Dark Magician would never harm him and asked the magician to let them past. To Shadi's astonishment the magician complied. Seeing Yugi's control over the Dark Magician, Shadi believed he may be the chosen one.
Shadi returned himself and Yugi to outside Yugi's soul. Before disappearing, he told Yugi his name and claimed to have not told it to anyone before.
After the group found Mokuba was back to normal, Croquet handed Yugi the other prizes on behalf of Pegasus, who had been taken to hospital. Yugi received the card "The Ties of Friendship", was crowned the King of Games and also received the 3 million dollar check, which he gave to Joey for Serenity's eye operation.
Kaiba thanked Yugi for saving Mokuba and insisted that they have a fair Duel someday to determine who is the better duelist. Yami Yugi congratulated Yugi on saving everyone. (In the English version, Yugi pointed out that he doesn't even know Yami's name. Yami replied that he has been called many things such as Pharaoh, Yu-Gi-Oh and Yami. Yugi refered to him as Yami and said he is glad to call him his friend, while Yami was proud to be one.)
As Yugi brought his grandfather home from the hospital, the group was confronted by Rebecca Hawkins. She accused Solomon of stealing her grandfather's "Blue-Eyes White Dragon" and challenged him to a Duel. At Kaiba Land, Yugi faced Rebecca in the Duel, as his grandfather was unfit to play. The Duel turned out to be an exact repeat of the Duel their grandfathers played a long ago over a drink of water. Like how Solomon surrendered back then as Arthur needed the water more, Yugi surrendered to teach Rebecca about the Heart of the Cards. Just then, Arthur arrived, showed that Yugi could have won, and explained why he surrendered. After Rebecca apologized, Yugi gave her the card, "The Ties of Friendship".
Mokuba arrived at Kame Game and informed Yugi and his friends that Kaiba's mind had been trapped in the Virtual World by The Big Five, while testing out a virtual reality machine that he created. Upon agreeing to help, Yugi, Joey, Téa, Tristan and Mokuba snuck into Kaiba's laboratory at the Adventure Game. Yugi, Joey and Mokuba got into pods to transport their minds to the virtual world, while Téa and Tristan kept guard.
Yugi, Joey and Mokuba appeared in a graveyard, where they were confronted by "Armored Zombie", "Clown Zombie" and "Dragon Zombie". They Summoned monsters to battle them, but the zombies kept reviving stronger than before. However Joey continued to attack them, until Yugi reminded him of his Duel with Bonz. So Joey played "Shield & Sword", dropping their DEF to 0 and Yugi finished off the zombies with "Dark Magician". Upon beating the zombies, they were each given a card displaying how much currency they have.
The trio spotted the fairy Iru, who guided them to a town. Here they heard that a prisoner, who may be Kaiba, had been taken to the Cave of Death. They were unable to travel there due to the sandstorm and a townsman informed them that they would need a "Niwatori" in order to cross that desert. Upon searching the town, they found a battle competition with "Niwatori" as a prize.
Yugi and Mokuba watched Joey Duel Madam Butterfly in the Coliseum. Once Joey found out that Madam Butterfly was Mai Valentine, Yugi and Mokuba ran over to them and explained what happened to Kaiba. Offering to help, Mai got her "Harpie Lady" to snatch the "Niwatori" card from the Coliseum owner and the four of them ran for the desert. At the edge of the desert, Mai played the "Niwatori" card, producing four large birds for them to ride on.
Once they crossed the desert, they reached the template at the Cave of Death. Inside they found themselves in a maze and were chased by "Labyrinth Tank". Yugi used "Magical Hats" to hide them and transport them to another part of the maze, where they met Iru and Edina. Iru guided the group to the exit, but it was guarded by "Gate Guardian". Yugi and Joey together Summoned "Black Skull Dragon" and equipped it with "Dragon Nails", making it strong enough to defeat "Gate Guardian". Outside the maze, a rescue party arrived and took Yugi and his friends to the palace as a reward for saving Edina.
At the palace Yugi and his friends learned that Edina was the queen of the land. (In the English version, she was a princess.) Edina informed them of a ritual where they must offer sacrifices to the Mythic Dragon. They learn that Edina is to be this kingdom's sacrifice and Kaiba is to be another kingdom's. Edina tells them of a legendary flying machine which can access the castle where Kaiba is and how she believed that Yugi and his friends are prophesized heroes who will destroy the Mythic Dragon. Yugi, Joey, Mai and Mokuba agreed to help and were given hero costumes to wear.
On one of the battlements, they were attacked by monsters who were after the sacrifice. Yugi, Joey and Mai unsuccessfully tried fighting them off. However Mokuba, who had previously swapped clothes with Edina, was kidnapped instead. While trying to find a way to save Mokuba, Yugi noticed a recent storm had revealed the outlines of the flying machine on the floor below them. Yugi asked Edina how long ago the legend involving the flying machine took place. With the unlikelihood of the machine still working and not enough time to dig it up, Yugi hinted to Joey that they needed to restore it to the condition it was 1000 years ago, prompting Joey to use "Time Wizard" to take the machine back 1000 years.
Yugi, Joey and Mai flew the airship up to the castle. On the way they were attacked by monsters, which they countered by Summoning their own monsters. Yugi was attacked while his "Dark Magician" was too far away to save him. However Iru, blocked the attack, sacrificing itself. Yugi then played "Swords of Revealing Light" to block attacks. Angry over Iru's death, Yugi switched to Yami Yugi, who led the group to the castle.
As Yami, he managed to regroup with the Kaiba brothers and defeat The Big Five's "Mythic Dragon" in the final stage by Summoning "Dragon Master Knight". Shortly after Edina thanked them and revived Mai, Joey, Mokuba and Iru, the group returned to the real world.
Grandpa feared for his business, the Kame Game, when the new game store, the Black Clown opened in Domino City. He ordered Yugi to stay away from the new shop. However Yugi and Téa passed it on the way to school later. Yugi received a flyer for a new game Dungeon Dice Monsters, but Téa dragged him away after he blushed at the lady handing out the flyer.
At school, they met the new student, Duke Devlin, the owner of the Black Clown. Joey was jealous of Duke's popularity and challenged him to a game of Duel Monsters. Yugi objected to the condition that Joey and Duke both use Decks from packs they open on the spot. Joey lost the televised Duel and in keeping his end of the bargain had to do whatever Duke said. Yugi became disgusted after Duke forced Joey to wear a dog suit and behave like a dog, so he switched to Yami who challenged Duke to a Duel. Duke accepted if they play Dungeon Dice Monsters instead of Duel Monsters and should Yugi lose he must relinquish his title of "King of Games" and give-up playing Duel Monsters.
Unfamiliar with the rules, Yami got off to a rough start. His chances did not improve as Duke revealed that he designed Dungeon Dice Monsters with Pegasus' aid. Duke blamed Yugi for Pegasus' disappearance after Duelist Kingdom. Yami used his innate gaming skills to turn the tables on Duke. Yami succeeded in calling "Dark Magician", which Pegasus had added to the game, and used it to defeat Duke.
After the game, Duke, Yugi and Yugi's friends went to Duke's office. Duke lamented that his dream has been crushed as nobody would want to play Dungeon Dice Monsters now. However Yugi assured him that it was a great game and his friends agreed. Duke apologized for how he had treated them and they agreed to be friends.
Yugi replaced the brown rope around the Millennium Puzzle with a chain, which Yami Yugi complimented and offered him advice on impressing Téa, who was waiting for him. Embarrassed, Yugi asks what he was talking about. As Yugi left the room, his mother asked who he was talking to. Yugi replied that it was nobody and dashed off, telling Yami to stop picking on him, as he offered to help make Téa like him. (The Yugis talking about Téa and the scene with Yugi's mother were removed from the English version.) Yugi met up with Téa and left for school with her. (In the English version, they were going to a soccer game) Yugi told her about the Yami Yugi; that he lives in the Millennium Puzzle, is worried about his destiny and has no memory of his past.
On the way to school, Yugi bumped into Bandit Keith, who was possessed by Marik Ishtar and disguised as a fortune-teller. Falling for the disguise, Yugi reluctantly let him hold the Millennium Puzzle in order to read his future. Keith knocked over the table at Yugi and Téa and ran off with the Puzzle. Yugi and Téa split-up to find him. In his search, Yugi followed a series of arrows, although he knew it was a trap, he felt that he had no other choice. Yugi caught-up with Keith, who had the Puzzle bolted to a wall. According to ancient rules, Marik had to win the Puzzle in a Duel, so he challenged Yugi to a Duel through Keith. Yugi was unable to switch to Yami during the Duel and quickly realized that Bandit Keith was his opponent after seeing he used a Machine Deck.
Yami Bakura sensed an evil presence and pinpointed it to the Duel. Seeing Keith controlled, Yami Bakura used the Millennium Ring to break Marik's control. Keith struggled to resist being repossessed, but Marik took control long enough to have Keith smash the Puzzle. Bakura swung down from a rope, knocking Keith unconscious. Bakura then collected a piece of the Puzzle and sealed a fragment of his soul inside it, before returning it to Yugi. Keith regained consciousness and continued to struggle with Marik's mind control, setting fire to the warehouse in his confusion. Unable to remove the piece of the Puzzle connected to the wall, Yugi stayed in the burning building to reassemble it. After inserting the last piece he collapsed and goes unconscious from the heat , but was rescued by Tristan and Joey and was taken to the hospital.
Worrying about how the Puzzle almost got stolen, Yugi took time to talk with Yami and discovered that Yami has no idea of who he once was, as he has lost all his memories. The duo suspected that their new enemy is in possession of a Millennium Item.
To try and help Yami regain his memories, Yugi asked Téa to spend time with Yami. He asked Téa out, but switched to Yami just before the date. Not expecting this Yami started shouting into the Puzzle at Yugi, until he was noticed by Téa. On the date, Yami and Téa learned from Ishizu Ishtar that Yami was once an Egyptian pharaoh and that Yugi had to enter the upcoming Battle City tournament to stop their new enemy.
While talking with Téa, about Duel Monsters at school, Téa asked which card best suited Yugi, assuming he would pick "Dark Magician". However Yugi explained that while "Dark Magician" is powerful, "Maha Vailo" better suits him, as it's not the strongest card, but it had hidden power. He would have liked to have picked "Dark Magician", but thought it's better suited to the other Yugi.
Yugi spotted Joey trying to get a rematch with the Rare Hunter, Seeker, who had won his "Red-Eyes Black Dragon". Yugi noticed his robes were the same as the ones Bandit Keith wore, while he was possessed. Seeker refused to face Joey again, but challenges Yugi to a Duel. Yugi accepts and switched to Yami, who won and took back Joey's "Red-Eyes Black Dragon". Marik then used Seeker as his puppet to communicate with Yugi. He introduced himself, told Yugi how he's after the power of the pharaoh and warned him that there are more deadly Rare Hunters. Yugi offered Joey back the "Red-Eyes", but Joey refused, saying he will wait until he's a true duelist before earning it back.
Yugi was lured into a tent by a harlequin and confronted by the Rare Hunter, Arkana. As Yami Yugi, he faced Arkana in a Duel, where the loser's feet got cut off by a buzzsaw. (In the English version, they got sent to the Shadow Realm by energy disks.) Yami won the Duel, but Yugi then took over and saved Arkana from the buzzsaw (energy disk in the English version).
At the canal side, while Yugi spoke with Yami about recent happenings they were confronted by another Rare Hunter, Strings. Strings was under Marik's complete control and dueled Yami Yugi using the Egyptian God Card, "Slifer the Sky Dragon". Yami won the Duel, earning "Slifer the Sky Dragon" through the Ante rule. Kaiba, who had appeared during the Duel challenged Yugi to a Duel on the spot, but Marik warned Yugi that he was going to take control of Joey. Yugi declined Kaiba's challenge as he had to find and save his friend.
As Yami Yugi searched the city for his friends, with Kaiba's help, they defeated the Rare Hunters Umbra and Lumis twice, gaining enough Locator Cards to qualify for the finals and also located Joey at Domino Pier.
At the Pier, Yugi was forced to duel Joey, who was possessed by Marik. Each player had their ankles chained to an anchor, which would drag them underwater to drown after the timer reaches 0. The only way for either player to save themself was to defeat their opponent, which would open a box, giving them a key. Yami made the first few of Yugi's moves, but Yugi insisted that he should fight this battle himself. Through talking to Joey and using "Red-Eyes Black Dragon" to remind him of his promise to become a true duelist and even giving him the Millennium Puzzle, Yugi managed to get Joey's subconsciousness to ignore Marik's commands. Yugi managed to fully snap Joey out of Marik's control shortly before forcing himself to lose. With Joey back to normal, Yugi told Marik that he was the true loser of this Duel. Yugi let his Life Points fall to 0 and collapsed, releasing Joey's key. However Joey managed to force the Duel into a Draw, releasing Yugi's key too. Using the chain, Joey swung to Yugi's side of the field and grabbed his key, before the anchor dragged them both down. He unlocked Yugi, who floated to the surface and was brought ashore by Tristan. Serenity dove in with the other key to save Joey. Joey later apologized and returned the Millennium Puzzle. Yugi thanked Yami for trusting in him and Yami said that Yugi has taught him the strength behind kindness and that one day Yugi will surpass him in every way.
Afterwards Mai gave Yugi and his friends a lift to the finals.
Yugi, Joey, Mai, Téa, Tristan, Duke and Serenity arrived at the KaibaCorp Stadium for the finals. Yugi was suspicious of the finalist Marik, who is under the guise "Namu", and Ryo Bakura, who should be in the hospital. Téa cleared any suspicion of Namu, by informing Yugi of how he saved her, Joey and Bakura earlier. Shortly after Odion Ishtar, pretending to be Marik arrived, everyone boarded the blimp, where the finals took place.
As Yugi prepared for the finals in his room, he added "Slifer the Sky Dragon" to his Deck, thinking he was going to need it to face Marik. He also suspected Bakura had come into contact with the Millennium Ring again.
Yami Yugi faced Bakura in the first of the quarter-finals on the Stratos Dueling Arena. Yugi's suspicions were confirmed as they faced Yami Bakura. When Bakura was one turn away from winning with "Destiny Board", the two Yugis agreed that they had to use "Slifer the Sky Dragon" to defeat him. Yami Yugi Summoned "Slifer", but Marik switched control of Bakura's body from Yami Bakura to Ryo, who was too weak to withstand the attack. However Yami Bakura disagreed with Marik's plan and took control of Ryo's body. He invited Yugi to attack him, refusing to let his host die. Yugi won the Duel, knocking Bakura unconscious and in leaving him need of medical attention.
During the intermission before the next Duel, Yugi unsuccessfully tried to get Kaiba to make an emergency stop to take Bakura to a doctor. Yugi went back to his room and began examining his Deck. He was interrupted by Shadi, who told him how the Egyptian God Cards were created and why he must stop Marik from getting his hands on them.
Joey defeated Odion, who was still pretending to be Marik and exposed him as a fake. Subsequently Namu was exposed as the real Marik and Yami Marik took control of his body. Marik confronted Yugi, saying the battle for the Pharaoh's power had just begun.
After losing to Kaiba, Ishizu Ishtar told Yugi of the Ishtar family's history and gave him the Millennium Necklace, as he was going to need all seven Millennium Items to recover the Pharaoh's memories.
That night Yugi was woken by Téa, who reported Bakura has gone missing. They discovered he was dueling with Marik and saw him lose shortly after they arrived.
The Battle City blimp got sucked into a mechanical fortress in the sea, by Noah Kaiba. Yugi, Joey, Tristan, Téa, Serenity, Duke, Kaiba and Mokuba exited the blimp, where they were greeted by a projection of the Big Five, who explained that they got trapped in the Virtual World, after they failed to trap Kaiba there, during the Legendary Heroes game. For that they hate Yugi and his friends for helping Kaiba. Having Kaiba as a common enemy, Noah uploaded their minds into his computer system. Using an altered form of Duel Monsters, they planned to face the gang in order to claim possession of their bodies, so that they may exist in the real world.
Yugi was transported to a pond, where he was faced by Gansley, who had taken the form of "Deepsea Warrior". Before dueling Gansley, Yugi changed to Yami Yugi, who Gansley identified as "Type-B". During the Duel, Yugi noticed that their Deck Master, Kuriboh was trying to tell them something. As Yami was about to lose, Yugi took over and used Kuriboh's Deck Master effect to save them. Shortly afterwards, Yugi collapsed so Yami took back control and won the Duel.
The Yugis entered a hallway afterwards. Although they were aware there were traps behind some doors, Yugi ran through one, after hearing Téa scream, but was thrown back by an attack. Yami draw the Level Star of the door to Yugi's attention, so Yugi Summoned a monster of a higher Level, "Winged Dragon, Guardian of the Fortress" and has it launch an attack into the doorway. They entered the doorway and wound up repeating the same process Realizing it was because they keep choosing the Level 1 door, they started attacking different Levels. The final door had the 2000 ATK, Level 4 monster, "Flash Assailant", backed up with a series of face-down Magic or Trap Cards. Yugi used "Heavy Storm" to clear the face-downs and "4-Starred Ladybug of Doom's" effect to destroy "Flash Assailant".
Yugi arrived at the scene of Téa's Duel, but was held back by a wall of ice. "Dark Magician" was taken from his Deck and Summoned to Téa's field, after she played "Sage's Stone". Attacking with both "Dark Magician" and "Dark Magician Girl", Téa defeated Crump, causing the ice around her to disappear. Yugi rushed to her aid and gave her his coat. Together they walked though the ice region and entered a door, taking them to a courtroom, where Joey was dueling Johnson.
Yugi correctly suspected that Johnson had rigged the outcome of Joey's luck based cards. Although Noah attempted to disqualify Johnson, Joey insisted that they continue with the game unrigged. After Joey won, he, Yugi and Téa exited though another door.
The trio found their way to Duke, Serenity and Tristan's Duel against Nezbitt. After the Duel, the gang tried to find Tristan, before the Big Five took his body. They briefly met up with Kaiba and Mokuba, but were attacked by Nezbitt in possession of Tristan's body. The real Tristan in the body of a robot monkey helped them fight the imposter. However Nezbitt kidnapped Mokuba and Kaiba took off after him, leaving the others think about what to do with the monkey, not knowing it was Tristan.
The group took a pick-up truck to go after Kaiba. On the way, they found out the monkey was Tristan after he accidentally flipped a switch, allowing him to speak normally.
After watching Kaiba duel Leichter, Yugi and Téa went with Kaiba to help him find Mokuba. The others tried to follow, but the tunnel disappeared, before they could enter.
Inside the tunnel Yugi and Téa got separated from Kaiba, and found themselves in a simulation of Kaiba's mansion back when Seto Kaiba got adopted. Yugi found a picture of Kaiba's father, Gozaburo, with Noah, shortly before meeting up with Kaiba again. Noah then showed the three of them a projection of the past, where Gozaburo showed Noah a picture of Seto, who Noah had to be able to compete with in order to run KaibaCorp.
Noah transported Yugi, Téa and Kaiba back to their friends, where they were confronted by the Big Five, now all sharing possession of Tristan's body. Yugi and Joey teamed-up to duel them in order to win back Tristan's body. Although Yugi and Joey won, the Big Five attempted to steal their bodies, but Noah took them away, along with Tristan's body, before they could.
Since Noah designed the robot monkey, Yugi and his friends searched it for clues. Yugi pushed a red button, which transported them to a virtual Kaiba Land. From there the gang took a handcar through a subway and wound up on the scene of Noah and Seto Kaiba's Duel.
Noah won and turned Seto and Mokuba to stone. This caused Yugi to get mad and change to Yami, who accused Noah of foul play, as he had used Mokuba as a shield to help him win. As Yami, Yugi combined his Deck with Seto's and continued the Duel. Noah gradually turned Yugi's friends to stone as Yami dueled, until none of them were left. Yugi then offered Yami support and took him to his soul room. Inside he brought Yami to a room containing his recent memories, where everyone, who had been turned to stone offered their support. Back in virtual reality, Yami imagined Yugi's friends giving him the cards drawn by "Card of Sanctity". With them, Yami Summoned Kaiba's three "Blue-Eyes White Dragons" to win the Duel against Noah.
After the Duel, Noah attempted to steal Yugi's body and escape to the real world, but the power of the Millennium Puzzle forced him back. After Noah found out that Gozaburo had been using him, he tried to help everyone escape the virtual world and took them to a virtual Domino City. The group got separated and met-up again, minus the Kaibas. Having realized Noah double crossed them, Yugi started to blame himself for trusting Noah.
Gozaburo had monsters attack Yugi and his friends as they looked for a way out, but Yugi and Joey fought them off by Summoning monsters from their Decks. Noah, having stolen Mokuba's body and escaped to the real world, organized a missile attack to destroy the fortress, including the servers for the virtual world. After having a change of heart, he contacted the group and explained that they must get out out quickly before the virtual world is destroyed.
Noah told them to go the arcade. Yugi, Duke and Joey fought off more of Gozaburo's monsters, while Téa, Serenity and Tristan went there. When Yugi, Duke and Joey got to the arcade, Noah asked Yugi to go and get Seto before returning himself.
Yugi complied and went to the KaibaCorp building, catching Seto shortly after he beat Gozaburo in a Duel. Gozaburo took the form of a monster and chased the two. Noah instructed them to jump off the building. With no other option they complied and awoke in the real world, before hitting the ground.
Yugi, Kaiba and Mokuba ran to escape the fortress before the missile strike and were helped onto the moving blimp by Joey and Tristan, shortly before the fortress got destroyed.
====Battle City finalsEdit====
The KaibaCorp blimp took the finalists to the Duel Tower for the Battle City finals. Yugi switched to Yami Yugi for the Battle Royal to determine match-ups and wound up with Kaiba as his opponent.
Yugi tried to stop Joey from dueling Marik. However Yami reminded him that Joey accepted the Duel knowing it would be a Shadow Game and nobody can stop such a game. (In the English version, Yugi worried for Joey and wondered if there was something they could do to help. However Yami assured Yugi that this was Joey's fight and he can win with their support.) After Joey lost, Yugi screamed that it's a lie. (In the English version, he said that he won't lose Joey to the Shadow Realm.) Later at Joey's bedside, he begged for him not to die. (In the English version, he blamed himself, saying that he should have dueled Marik instead.) Out in the hallway, Yugi cried more and considered stopping dueling, but Yami convinced him that they must not give-up and let Marik win. Yami got the idea to use the Millennium Necklace to see what happens. He and Yugi then used it to look into the future, where they saw Yami and Joey preparing to Duel.
Yugi dueled Kaiba in the second semi-final as Yami Yugi. They managed to defeat Kaiba and afterwards found out Joey was okay to Yugi's delight. Yugi and Yami gained Kaiba's "Obelisk the Tormentor" card through the ante rule.
Yugi and Yami watched Joey duel Kaiba in a third place play-off. They both agreed that Joey was a great duelist and would have defeated Marik, had their Duel not been turned into a Shadow Game. The two them noticed the Millennium Puzzle acting strange and saw Téa's reflection in it. They left the Duel to find Téa, who was possessed by the original Marik to confront Yami Marik. At the top of the Duel Tower, they found Téa, Marik and Ishizu. Ishizu explained that Téa would be fine and that Marik's good side still lives on within Téa's mind.
Before facing Marik, Kaiba gave Yugi the card, "Fiend's Sanctuary", which Kaiba intended to use against Marik himself. Yami Marik and Yami Yugi's final Duel was a Shadow Game, where the regular Yugi and Marik were drawn from their bodies and floated next to them in spirit form. Yugi and Marik were bound by their wrists and ankles in darkness and parts of their bodies disappeared as their "Yami" selves lost Life Points. (In the English version, they were disappearing into the Shadow Realm.) If Yami Yugi lost, Yugi would vanish, and Yami would cease to exist.
Yugi encouraged Yami throughout the Duel. He even urged Yami to pay Life Points to keep "Fiend's Sanctuary" active, knowing it would make part of his body disappear. Yugi insisted that they must find a way to without causes the good Marik to disappear. However, the good Marik possessed Téa and told Yugi not to hesitate, he's prepared to die. He no longer blamed the Yugis for his father's death. (In the English version, Marik said not to worry about protecting him, he wants to defeat his dark side at all costs.)
Yugi was certain that Yami Marik was going to fuse with "The Winged Dragon of Ra" a second time in the Duel and reminded Yami Yugi that if he does that again, he will become a monster and have the weakness of a Monster Card. With that in mind, Yami Yugi managed to use "Ragnarok", which would destroy "Ra". As Yugi wondered if this would cause the good Marik to disappear, Odion appeared. Since Odion had been keeping Yami Marik away, his return allowed the regular Marik to regain some control of his body and urged Yami to attack. The Yugis continued to use the effect of "Ragnarok", which destroyed Ra and caused Marik and Yami Marik to switch places. With only 1 Life Point left, only Yami Marik's eye remained. Marik then surrendered causing Yami Marik to disappear and Yugi to win the Duel.
As the host, Kaiba congratulated Yugi for winning. (In the English version, he added that Yugi only won because Marik surrendered.) Marik informed Yugi that with his dark side gone, the souls of Mai and Bakura should be released and gave him "The Winged Dragon of Ra" due to the ante rule. Marik then showed Yugi the hieroglyphs carved on his back, explaining that the secret of the Pharaoh's power is written there, and whoever holds the three Egyptian God Cards can unlock that secret. With his mission complete, Marik handed the Millennium Rod and Ring to Yugi.
Kaiba announced that he was going to blow-up the Duel Tower and gave everyone an hour to evacuate. Yugi and his friends returned to the Battle Ship and found that Mai and Bakura were okay, but there was no sign of the Kaiba brothers on the blimp. With the Battle Ship damaged from escaping Noah's fortress and no one able to find the Kaibas, everyone else boarded the KaibaCorp helicopter. As they left, they saw Kaiba and Mokuba had escaped in their Blue-Eyes White Dragon jet.
Back in Domino City, Yugi and his friends said goodbye to the Ishtar family, Duke and Mai. Afterwards, back in Kame Game, Yugi and Yami Yugi assembled a Deck and included the "Red-Eyes Black Dragon" Joey gave them. At sunrise, the Yugis met Joey at the plaza for a final Duel to conclude their Battle City.
Between classes, Yami took control of Yugi's body and skipped out of school to go to the museum, with Egyptian God Cards to uncover his memories. Yugi asked why they were going alone. Yami replied that it would be too depressing to say goodbye and just wants Yugi to see him off. (In the English version, there was no mention of why they were going alone. Instead Yami said that he felt the Egyptain God Cards pulling him to the museum.) However, Téa, Joey and Tristan caught up with him outside the museum and reminded him that they are a team. Inside Yami held the Egyptian God cards up to the tablet, but something held him back. The group heard a scream and dashed outside, finding a large number of living Duel Monsters in the city.
Later at the Kame Game, as Yugi and his friends watched Kaiba on TV explaining that he wasn't responsible, there was a break-in and the Egyptian God cards were stolen by motorcyclists from Doma. They quickly rushed outside and saw the Gods appear in the city. Yugi wondered who could have Summoned them as only someone with a connection to the Millennium Items can Summon the Egyptian Gods. The thieves then appeared before them, demanding that Yugi follow them if he wants to get the God cards back. Yugi changed to Yami and wound up dueling one of them, Gurimo. Gurimo used the soul stealing card "The Seal of Orichalcos" and was even able to Summon "Obelisk the Tormentor" through its power. Yugi still managed to defeat Gurimo, causing his soul to be sealed in the card. Afterwards Yugi took his necklace containing a fragment of the Orichalcos stone. As a reward for his victory, Rafael released the souls of Rex and Weevil, which Gurimo had previously captured using "The Seal of Orichalcos".
On the street, Yugi, Téa, Joey and Tristan found Rex and Weevil and discussed the bikers, who had stolen their souls and Yugi's God cards. Rex and Weevil pretended to agree to help them, but secretly planned on getting the God cards for themselves.
After leaving Rex and Weevil, Yugi and his friends met Rebecca Hawkins, who claimed that Yugi is now her boyfriend and took them to the museum to see her grandfather Arthur. From researching the origins of Duel Monsters, Arthur confirmed that Yugi was indeed sharing a bond with an Ancient Egyptian pharaoh and informed them that pharaoh saved the world when Ancient Egyptian sorcerers harnessed real monsters' powers by sealing them in tablets, like Duel Monsters. He also showed them photos from what he believed was Atlantis, showing carvings of Duel Monsters, proving that the origins of Duel Monsters dates back further than 3000 (5000 in the English version) years in Egypt to at least 10000 years ago in Atlantis. Arthur told them that he believes there is a parallel dimension where Duel Monsters are real. Since the pharaoh saved the world the last time people conjured these monsters, Arthur believes Yugi is to save the world this time, since the pharaoh has been reborn in him. Not certain what to do next, Yugi gave Arthur the stone he had taken from Gurimo for him to test. Outside the museum, to Yugi's embarrassment, Rebecca gave him a kiss before leaving. Shortly before leaving himself, Yugi thought that he heard someone calling for help, but couldn't see them anywhere.
As Yugi went to sleep that night, he heard the voice calling for help again. The Millennium Puzzle activated and the two Yugis were sent to the chamber inside the Millennium Puzzle. They heard the voice calling for help again and searched to see if they could find who it was. They eventually found Kuriboh, who led them to a room they'd never been to before. They heard the voice again and followed it, causing them to be transported through a vortex to the Duel Monsters Spirit World.
Yugi and Yami found themselves hovering above a castle. They flew down into it and met Dark Magician Girl, who told them that both worlds were in danger. She explained that the two worlds rely on each other for survival, but now a gateway has been opened between the two worlds and the great beast, who feeds on the life force of humans and spirits will consume them all. Yugi and Yami agreed to help them, so Dark Magician Girl took them to three dragons trapped in crystal. According to legend, three warriors should be able to free them. Believing Yugi to be one of the warriors, she instructed the Yugis to remove a sword from one of the dragons. Yugi and Yami pulled the sword out, freeing the dragon, Timaeus.
Yugi woke-up in his bed shortly afterwards. He saw a strange light phenomenon trapping monsters outside. He ran to the plaza to see what it was and met his friends there. The monsters were absorbed into a crystal, which shattered, revealing an eye, which shot a twister at Yugi. However Yugi's Duel Disk began to glow as the card, "The Eye of Timaeus" appeared in it. Using it, Yugi Summoned Timaues to attack and destroy the eye. The Dark Magician Girl then appeared next to Yugi and informed him that the battle is just beginning.
While showing his friends the card, Yugi received a package from Industrial Illusions, containing a videotape and the card, "Illusion's Key". He was initially reluctant to watch the video, remembering the last one Pegasus sent him. After deducing Pegasus can't seal souls, since he no longer has the Millennium Eye, Yugi and his friends watched the tape. Pegasus offered some explanation for the recent events, but since it was too risky to leave the information on tape, he asked Yugi to meet him in person and arranged a jet for Yugi and his friends to come to California and bring the "Illusion's Key" with them.
The group took the plane to San Francisco, where a limousine was provided to take them to the Industrial Illusions headquarters. Inside the limousine, Yugi noticed "The Eye of Timaeus" lighting up as Kaiba freed Critias elsewhere. However the limousine took the group to a desert and the driver abandoned them at a gas station. At the station, they were approached by another motorcyclist gang looking for trouble, but Mai Valentine appeared on a motorbike and fought off the bikers, causing a fire. Tristan drove Yugi, Joey and Téa in the limousine away from the station before the gasoline pump caused an explosion. Mai also escaped on her motorbike and drove away. The limousine broke down, while still in the desert, leaving Yugi and his friends stranded. Using Téa's femininity while the boys hid, they were able to hitch a ride from a truck driver to Industrial Illusions.
When the group finally at the Industrial Illusions headquarters, they were locked in by Mai, who revealed that she was with Doma and had captured Pegasus' soul in a "The Seal of Orichalcos" card, before challenging Joey to a Duel. During the Duel, Yugi's "The Eye of Timaeus" card once again lit-up as Joey was sent to the Spirit World to free Hermos. Fearing Mai would lose, Valon broke-up the Duel and the members of Doma fled.
Yugi and his friends were then joined by Duke, Rex, Weevil and Kaiba. Using the card "Illusion's Key", Yugi was able to open a secret room, where they encountered a holographic recording of Pegasus. Pegasus told them about Doma's involvement in historical events and told Yugi where to find an exclusive card, he would need later. They found the card, "Legend of Heart", albeit blank at the time, within the room. Although, Kaiba decided not to stick with Yugi and his friends, they correctly guessed that he had the other Legendary Dragon, "The Fang of Critias".
Duke gave the gang a lift to Arthur Hawkins' house to look for clues on what to do next. By the time they got there, Arthur had been kidnapped and the house was blown-up. Rebecca flung herself around Yugi and explained what happened. The group went into Arthur's mobile home and discussed what happened. Rebecca returned the Orichalcos stone, Yugi had lent to Arthur. While the others prepared something to eat, Yugi and Rebecca stepped outside to talk. Rebecca showed Yugi a card and note from Rafael she found after the explosion. Rafael's note told Yugi to come alone to Death Valley. (In the English version, it told Yugi to go there if he wanted to see Arthur again.) Later that night, Yugi borrowed Rebecca's horse, Copernicus, to go there.
Yugi dueled Rafael as Yami Yugi at Death Valley, but still accompanied Yami in spirit form. Yugi was relieved when Rafael said that he had no intention of playing "The Seal of Orichalcos" in this Duel. However Rafael used "Exchange" to give the card to Yugi later on. Yugi urged Yami not to use that card, no matter what happens and Yami agreed. However, they reached a point, where Yami felt he was going to lose, unless he played the Seal. Despite Yugi's objections, Yami played it and Yugi's spirit form left him alone.
Yugi was unable to contact Yami for the rest of the Duel, as he was trapped behind a seal. He unsuccessfully tried pleading with him to not sacrifice his monsters, including "Dark Magician Girl", who they made a promise with. Yami went on to lose the Duel and was about to lose his soul to "The Seal of Orichalcos". Using the power of the Millennium Puzzle, Yugi broke the seal that was holding him back and appeared next to Yami again. Since "The Seal of Orichalcos" only takes one soul, Yugi pushed Yami aside and let the seal take him instead.
Yami traveled to the Stone Wilderness, where spirits are roam, in the hopes of contacting Yugi. He managed to find Yugi and apologized for what happened. Without Yugi, Yami said the darkness inside him is starting to grow. He was afraid that Rafael might be right that he is evil and feared getting his memories. Yugi reminded Yami that he has been locked away. Yami tried apologizing again, but Yugi said that he didn't want his pity. Yugi asked if Yami only came here to demoralize himself. (In The English version, he said if Yami truly is evil, there's only one thing to do.) A Duel Disk appeared on Yugi's arm and he challenged Yami to a Duel. Yugi knew that he would have to duel Yami sooner or later and if Yami's heart has become dark Yami shall lose. (In the English version, Yugi said that Yami doesn't deserve to be a part of this world and must pay for what he has done.) Yami reluctantly accepted the Duel.
Both Yugi's drew the same cards in the same order, so Yugi used "Sangan" to shuffle his Deck and "Card Destruction" to reset their hands. Yami stated that the Duel was meaningless. However Yugi explained that Yami's weakness is the darkness in his heart, he is arrogant and warped by his sense of pride. With only one value, it's impossible for Yami to see other people's pain. (This explanation is removed from the English version.) Since he was a mirror reflecting Yami's dark side, Yugi had "The Seal of Orichalcos" in his Deck. Yugi used it and proceeded to use the same strategy Yami used against Rafael, sacrificing his monsters to win. Yami realized that this is what he looked like in the Duel against Rafael. He refused to lose, as it would prevent him from saving Yugi. He managed to counter Yugi's strategy and win. Yugi was pleased that Yami won and said that in defeating him Yami defeated the darkness in his heart. Before disappearing again, he urged Yami not to give up and said that he will always be with him.
When Kaiba and Yami were dueling Dartz, the leader of Doma, Dartz Summoned four "Mirror Knight Tokens". When Kaiba tried destroying them, he instead caused their helmets to break revealing that they had taken the form of people whose souls had been lost to "The Seal of Orichalcos", including Yugi, Joey, Mai and Pegasus. Dartz claimed that destroying the Tokens would result in destroying their souls. The "Mirror Knight" Yugi tried to resist when Dartz made him attack Yami. Yami refused to attack any of the Tokens as it would risk killing his friends. Kaiba was convinced nothing would happen if the Tokens were destroyed and attacked the Joey one, but the Yugi one used his effect to block the attack at the cost of his shield. Yami was given another opportunity to destroy the Tokens. He was reluctant, but Yugi insisted that Yami attack and not worry about him, as he has a more important mission to focus on. (In the English version, Yugi said that he would be fine.) However, Yami still refused to attack. After playing "Orichalcos Tritos", the "Mirror Knights" were unable to defy Dartz and he had Yugi attack Yami. Eventually Kaiba got the opportunity to destroy the Tokens. Yami tried to stop him, but Yugi insisted that he would be fine and Kaiba continued.
Yugi's was soul was trapped in a bubble being sucked into The Great Leviathan. The souls of people, who were recently taken by "The Seal of Orichalcos" floated in bubbles near him. After Yami defeated Dartz, the Legendary Dragons now in their Legendary Knight forms, released the souls of the chosen duelists; Yugi, Kaiba and Joey. Yami informed Yugi that the knights had freed him and Dartz had disappeared into a vortex after the Duel.
Roland alerted Yugi, Kaiba and their friends about Atlantis rising from the sea. Yugi, Kaiba and Joey opted to travel through the vortex Dartz used, suspecting it would take them to Atlantis to face him. Téa objected as they could be walking straight into Dartz's trap, Yugi convinced her that they must go to save the other lost souls. Inside the temple where the Duel took place, the Millennium Puzzle started to glow and led Yugi to the location of the Egyptian God cards. However they were powerless as Dartz had already sucked their energy into the leviathan. Yugi caught up with Joey and Kaiba and returned their Legendary Dragon cards before the three stepped into the vortex. The trio emerged on Atlantis and Yugi switched to Yami. They found that Dartz had left his body and combined with The Great Leviathan, to compensate for not getting the souls of the chosen duelists.
As Yami, he, Kaiba, Joey and an army of Duel Monster Spirits battled the leviathan. However the leviathan's tendrils pulled the three chosen duelists inside it. Yugi appeared next to Yami and suggested that they might be able to fight back by calling to the other people trapped inside. Taking Yugi's advice, Yami called on everyone else to focus on the light in their hearts and pass that strength onto him. Using it he Summoned the Egyptian Gods and freed the chosen duelists from the leviathan. Thinking the Gods might need his help, Yami returned control of Yugi's body to Yugi an flew up to the Gods in spirit form. Yugi cheer for Yami as he watched him and the Gods battle and defeat the Leviathan.
Yami returned to Yugi back on Atlantis just as it started to sink. As Yugi was about to leave through the vortex after Joey and Kaiba, Yami called him back and the duo were confronted by Dartz and The Great Leviathan in a smaller form. After Timaeus failed to destroy the leviathan, Yami advised Yugi to run, but Yugi refused to leave and helped Yami argue against Dartz's ideology. The Leviathan turned into a black whirlwind and surrounded Yami. Yugi tried to help Yami, but Yami insisted it was his fight and he must prove the darkness in his heart is gone. Focusing on that the leviathan disappeared.
Yugi and Yami saw that Dartz's evil side was now gone as was accompanied by Ironheart, Chris and Skye. Ironheart and Chris thanked the Yugis and told them to return through the portal where a new future was waiting for them.
Yugi washed-up on a shoreline afterwards, where they were greeted by Dark Magician Girl and the Legendary Knights, who thanked them for their help. Yugi's friends, who had escaped Dartz's temple in Kaiba's helicopter, flew down to greet him, relieved that he had survived.
Yugi, Kaiba, and all of Yugi's friends prepared for Kaiba's ultimate tournament, the KC-1 Grand Prix Championship. The winner of the tournament would face Yugi Muto in an attempt to claim his title as the world Duel Monsters champion.
On the opening day, while Yugi and his friends are watching a Duel between Rick and a CPU opponent, a hacker traps all the duelists and spectators inside the makeshift electronic stadium. The CPU opponent level has been altered to its highest of difficulty, and the only way for everyone to escape is to defeat the CPU in a Duel. Rick had mostly Dragon-Type Normal Monsters and almost no Magic or Trap Cards in his Deck. Yugi transforms into Yami and takes over, using "Heart of the Underdog"—a card Yugi had given Rick—and combined it with the effects of "Spirit Ryu" to win and free everyone.
Yugi didn't duel much in this season. He cheered for Joey and Rebecca throught the tournament. He dueled and defeated Vivian Wong, in order for her to cure Solomon Muto's back.
Yami faced Leon von Schroeder, who assumed the alias Leon Wilson, in the finals. Leon acted differently during the Title Bout and Yugi discovered that Leon only wanted to duel and defeat him to earn the respect of his family that Zigfried couldn't earn in his youth. Leon played an illegal card, "Golden Castle of Stromberg", that forced Yugi to discard half the cards in his Deck with every passing turn that Leon took and also infected a virus into the KaibaCorp computer system. Yami figures out a weakness in the card; He couldn't discard half the Cards in his Deck, having only 1 card left. He was able to destroy it and nullify the virus. With "Golden Castle of Stromberg" defeated, Yugi continued the Duel and played several Magic and Trap Cards before striking the final blow using "Dark Magician", "Necromancy", and "Diffusion Wave-Motion" to win.
Before heading to Egypt to finally unlock the pharaoh's memories, Yugi wanted to learn as much as he could. He asked his Grandpa to tell him about his adventure where he recovered the Millennium Puzzle from the Tomb of the Nameless Pharaoh. He was sad to hear that Grandpa didn't know the way back to the tomb, but Grandpa advised him to stay away from there. Obsessed with the Egyptian God cards, Grandpa pleaded with Yugi to leave them with him rather than return them. Yugi reminded him how the pharaoh was going to need them and Grandpa apologized. Before saying goodnight, Grandpa said that his own adventure was over and assured Yugi that he is the only one with the power to help the pharaoh recover everything he has lost. Holding the legacy of the pharaoh is no small task, he said and advised Yugi to take every challenge like he faces a game.
As Yugi slept, he dreamed he was talking with Yami, reflecting on how meeting each other had changed their lives.
Yugi was woken-up as he heard Rex and Weevil breaking in to steal the Egyptian God cards. They took a bag, not knowing it also contained the Millennium Items, and Yugi ran after them. By the time Yugi caught up, they had been knocked unconscious by Yami Bakura who had taken back the Millennium Ring.  Bakura returned the Items and God cards to Yugi, but insisted on keeping the Ring for himself. He tried to assure Yugi that they had the same goal; to bring the seven Millennium Items to the Millennium Stone. Taking control of Yugi's body, Yami ordered Bakura to stop poisoning Yugi's mind. Before parting Bakura said that in order to solve the riddle of the pharaoh's memory they will play the ultimate Shadow Game.
At the airport as Yugi prepared to board his flight, he unexpectedly met Joey, Téa and Tristan. He told them that they didn't have to come, but they insisted that they wouldn't miss this for the world.
At the airport in Egypt, Yugi and is friends were greeted by Ishizu, Marik and Odion Ishtar, who brought them to an underground cavern in the desert, where the stone tablets from the museum had been relocated. As Yami held the Egyptian God cards up to the tablet, his spirit was sucked out of Yugi's body and into the Memory World. The portion of Yami Bakura's soul that had secretly been sealed in the Millennium Puzzle was also sucked into the Memory World, taking the rest of Yami Bakura's spirit from Ryo Bakura with it. Yugi reported that Yami was no longer present in his heart or the Puzzle.
Shadi appeared and confirmed that the pharaoh had left Yugi. He informed them that the pharaoh has gone to a world of his memories, which was created 3000 years ago from the Pharaoh's experiences. Fearing Yami is in the same danger that sealed him in the Millennium Puzzle the first time around, Yugi, Joey, Téa and Tristan pleaded with Shadi to let them go to the Memory World to help Yami. Shadi explained that they must go through a doorway in the Millennium Puzzle to get there. Again Yugi insisted on going alone, but his friends wouldn't have it. Using the Millennium Key, Shadi brought the four them inside the Puzzle, where they began searching the labyrinth for the right door.
Yugi and company searched the inside of the Puzzle for a long time, but no no avail. Behind one of the doors they found Yami Bakura who turned into a monster and attacked them. After escaped Shadi informed them that that was the pharaoh's enemy in his true form. Sine the maze reflected the pharaoh's heart, Yugi eventually started to feel it tremble as Yami was in danger. (In the English version, the temperature changed as the pharaoh's emotions changed.) Yugi realized that rather than calling for the pharaoh, they needed to wait for the pharaoh to call to them, so he got everyone to sit together and concentrate. This caused to labyrinth to open a door to the Memory World.
Yugi, Joey, Téa and Tristan entered the Ancient Egyptian Memory World, where Yugi no longer had the Millennium Puzzle. Despite looking out of place, no one took any notice of them. They quickly learned that other people could not see them and trying to touch solid matter, resulted in them phasing through it. Unbeknownst to them, they had entered an RPG played by Yami Bakura and Yami Yugi, where they acted as non-playable characters.
The group found Bobasa, who like them could't be seen by most other people, but unlike them was able to touch objects. Chasing Bobasa led them to find Priest Seto saving Kisara. Recognizing him as the guy who looked like Kaiba from the tablet, they knew he worked for the pharaoh and followed him to the palace. Unlike other objects, they found that they couldn't phase through the palace gates. Bobasa reappeared and offered to help them.
The five of them fell asleep outside the palace until the gates finally opened as the pharaoh chased Thief Bakura on horseback, accompanied by the monster Ka Diabound and Slifer the Sky Dragon respectively. Yugi, Joey, Téa and Tristan ran after them and finally caught up with the pharaoh after he fell off his horse following Slifer's defeat. They were happy to find that the pharaoh could see them, as he asked Yugi in surprise if it was really him. By taking the pharaoh's hand, Yugi was able to give him some of his strength, enabling him to summon The Winged Dragon of Ra to battle Bakura's Diabound.
Ra initially defeated Diabound, but Yami Bakura, playing the RPG, used one of his Hourglass Tokens to turn back time to a few minutes previous. This time following Slifer's defeat, Diabound's attack smashed the ground below the pharaoh, causing him to fall into a chasm before Yugi and his friends could get to him. Yugi's friends briefly encountered Thief Bakura before being called by Bobasa to hide. Téa worried that the pharaoh may have lost his soul, since he just lost a Shadow Game, but Yugi reminded everyone that the world is built on the pharaoh's memories and since it still existed, he had to be okay.
The next day, Yugi, Joey, Téa, Tristan and Bobasa searched for the pharaoh along the River Nile. There they found Mana, who was able to see them and mistook Yugi for the pharaoh. When they started talking about looking for the pharaoh after Bobasa had found his cape, Mana realized that Yugi isn't the pharaoh. She quickly learned that they were his friends and joined their search party. The group were about to be attacked by Thief Bakura's men, shortly afterwards but Mana used her magic to raise the river and sweep the attackers away. As they continued their search Mana explained how only half her spells work, but Yugi told her how she resembled the card "Dark Magician Girl" and that if she kept practicing he's sure Mana could become as strong as the "Dark Magician Girl". Eventually the party found the pharaoh on the beach.
Yugi and his friends learned that Thief Bakura had taken the Millennium Puzzle from the pharaoh and was after the other Items too. The pharaoh told them that had only regained a fragment of his childhood memory and no one would tell him his real name. The pharaoh eventually left on horseback with Mana and asked that Yugi and the others return to their world and not get involved.
Tristan, who had secretly been possessed by Yami Bakura suggested that the pharaoh deliberately made himself lose his memory in order to forget information only he knew that someone would need to bring back the evil that he had locked away. Yugi and the others agreed that this must be his name, which had been erased from history. Yugi figured the pharaoh must have used it as a password to lock Zorc Necrophades away. Since the pharaoh was going to relive his battle with this creature, Yugi realized that without knowing his name, the pharaoh will lose this time. Determined to find out the pharaoh's name before the battle, they decided to go to the palace to see if there was some record of it.
This time at the palace, thinking to himself, Yugi asked the pharaoh to let them in it, and found he could pass through the palace gates. Inside the courtyard, he suggested that they split up to search and meet back in an hour. As they searched, Yami Bakura used another Hourglass Token to temporarily freeze time.
The five of them met-up again, finding Bobasa had eaten all the food in a storage room. Despite this, he was still hungry and couln't move without eating again. Tristan, who was still possessed argued that Bobasa was no help and they should leave him. However Yugi pointed out that he had helped them find the pharaoh. The others agreed and helped Bobasa find something to eat. After finding some grapes they pulled him outside and let him eat them. The grapes finally filled Bobasa, who said this allowed him to grant their wish. His body inflated, allowing him to float in midair. He invited them to get on his back, so he could take them to see the pharaoh's name. He flew them to the pharaoh's tomb at the Valley of the Kings.
The inside of the tomb was filled with traps. Remembering Grandpa's story about his visit to the tomb, Yugi knew traps operated and was able to guide his friends safely through. They reached the room where Grandpa found the Millennium Puzzle, but were unable to find any clues there, so they began searching for another room.
Joey accidentally leaned on a hidden switch, unlocking a passageway. Possessed, Tristan ran ahead of everyone else, but found the room was empty. To everyone's surprise, Tristan read the hieroglyphics on the floor claiming they said that whoever solved the Millennium Puzzle must return the wish that they were granted in order to pass. Yugi claimed that what he wished for could never be returned, but after some coaxing admitted that he wished for friends. Téa and Tristan were touched, having never heard this before. Tristan pushed Yugi onto one eye pattern on the floor and pushed Joey and Téa onto another, where he joined them. The floor apart from the two eyes and a connecting beam gave away, leaving the two eyes balancing on a stone needle below the middle of the beam. (In the English version a pit of shadows is added below the platform. In the Japanese, it's just a long fall.) The beam turned, positioning Yugi's eye at a door to another room. Yugi was reluctant to go through as it would have meant losing his friends. After calling Yugi weak, Tristan leaped from the platform to the doorway, causing the platform to go off balance. Joey and Téa jumped off the platform and grabbed onto the ledge. Yugi ran after them and jumped catching onto Joey. The three of them climbed up and entered the room.
Inside the room, they found the name written on a wall. Unable to read it, they just memorized the hieroglyphics. As they looked around for Tristan, they spotted and exit and followed it.
Yugi, Joey and Téa were taken to a chamber with two sides connected by a bridge. Standing at the other side was Tristan who revealed he was possessed by Yami Bakura and took on his appearance. At the same time, the room shook as Zorc was about to be resurrected elsewhere. Yami Bakura laughed that they weren't going to leave with the pharaoh's name, then formed a Duel Disk on his arm and challenged Yugi to a Duel.
Bakura explained that their Decks will be created from images of their mind and the order of the cards won't be revealed until they draw. Duel Disks and Decks then appeared on their arms. Bakura told Yugi that this would be a Shadow Game, so losing would mean losing his soul. (In the English version, Bakura instead said that it had been a while since they dueled, but this time Yugi doesn't have Yami Yugi to bail him out.) As they dueled, Yugi realized that the Deck created from images of his mind was much different than his real Deck.
Yugi intended to level up "Silent Swordsman LV0" under the protection of "Marshmallon" and "Marshmallon Glasses". However Bakura forced "Marshmallon" into Attack Mode, leaving Yugi the burden of defending it too. Whenever Bakura took the upperhand, he would often taunt Yugi about not being able to win without Yami Yugi. Bakura used "Cursed Twin Dolls" to remove his own Graveyard, filling his field with ghosts and "Counterbalance" to cause players to send cards from their Deck to the Graveyard equal to the number of cards on the field including the ghosts each turn. Since Bakura no longer had a Graveyard he was unaffected. Yugi used "Aria from Beyond" to use "Spirit Sword of Sealing" to temporarily remove "Silent Swordsman" from the game. Bakura's strategy left Yugi with one card in his Deck, "Gandora the Dragon of Destruction", which he drew and Summoned. Using its effect, "Gandora" destroyed and removed from play all other monsters on the field and then destroyed itself. This deactivated the effect of "Spirit Sword of Sealing" and returned "Silent Swordsman". Yugi used "Silent Swordsman", with 4500 ATK to attack and defeat Bakura.
Bakura said that he couldn't believe he lost to a "container". Before relinquishing control of Tristan's body, he laughed that Zorc had still been freed and they couldn't win if the pharaoh dies. After explaining to Tristan what just happened, the chamber started to collapse. The quartet exited through a tunnel leading them to the side of a cliff.
After sliding down the cliff, Yugi and his friends were attacked by hooded riders. Like how Yugi and Yami Bakura were able to form Duel Disks, Yugi realized that if concentrated hard enough, their thoughts could become real. With no time to fight the riders, they imagined that they could fly and took off to find the pharaoh.
As Zorc was about to throw a fireball at the pharaoh, Yugi and his friends arrived. Zorc instead threw the fireball at them, saying that they should have stayed in their own world. The group dodged the attack, but saw some of Bakura's soldiers approaching. Preparing to fight, Yugi conjured a Duel Disk and the Deck that he and Atem built. He Summoned the "Dark Magician", who the pharaoh now recognized as Mahad. Joey, Téa, Tristan and Mana, who was at the palace, Summoned more monsters to battle the soldiers.
With the Monster Spirits battling Zorc and the soldiers, Yugi and his friends gathered around the pharaoh. They told him that they had seen his name and remember what it looked like, but were unable to read it. However after seeing the pharaoh's cartouche, Anzu suggested that they concentrate on making the hieroglyphics appear on it. They all held their hands over the cartouche and tried this. Zorc tried to stop them by throwing another fireball in their direction, but Seto Kaiba appeared and used "Ring of Defense" to block the attack. Zorc launched another attack destroying the ring. Yugi and company managed to survive with the name engraved on the cartouche. The pharaoh declared that his name was Atem. Knowing this he was able to revive the Egyptian Gods and combine them into The Creator God of Light, Horakhty, who attacked and destroyed Zorc.
Yugi and Atem both found it weird having different names at first, having shared an identity since Yugi solved the Puzzle. Yugi said he felt a bit lonely, but it was okay. Even if their names are different, he said that they will still be a team. After saying goodbye to Priest Seto, Atem reached the end of his memories he could no longer exist in the Memory World, so he joined Yugi, Joey, Téa, Tristan and Kaiba to leave through an opening in the sky.
Yugi and the others awoke in the cavern they had entered the world of the pharaoh's memories from. Yugi found that Atem still residing in his body and received the Millennium Eye from Kaiba, who said he'd be needing it. Before they can question Kaiba on how he got it, they were interrupted by the appearance of Ryo Bakura, who was no longer possessed by Yami Bakura. As they left the Yugis took the Millennium Ring from Bakura and found the Millennium Scales and Key, left behind by Shadi.
The Ishtars began to guide Yugi and his friends to the Shrine of the Millennium Stone; The pharaoh's final resting place. They went on to a boat, where Yugi met up with Duke, Grandpa and Mokuba. On the boat, Marik told Yugi that Atem would have to lose in a Ceremonial Battle in order to move on. Joey and Kaiba both offered to Duel Atem, but Yugi declined their offers in favor of dueling Atem himself. He believed that this was something both he and Atem needed. Angrily, Kaiba showed Yugi a briefcase of cards and said that if he's dueling he might as well use a real Deck, but Yugi declined again, wanting to use his and Atem's cards.
The night before they arrived at the shrine, Yugi worked on his Deck. Téa came into Yugi's room and admitted that she didn't want Atem to go and asked how Atem felt about it. However Atem had been hiding within his soul room to give Yugi privacy while he made his Deck. As he constructed the Deck, Yugi reflected on how solving the Millennium Puzzle changed his life. Once he finished, he gave Atem privacy to construct his Deck.
The next day, everyone arrived at the shrine. This was the best time for the Duel as Zorc had just been defeated, Ishizu assured them and said the pharaoh will stuck in this time if they don't take this chance. Yugi placed the Millennium Items in the Millennium Stone. This caused the Eye of Wdjat to scan him for the pharaoh's soul and split them into two bodies. Yugi and Atem walked to opposite sides of the cavern and prepared to Duel.
Atem choose not to hold back and quickly Summoned the three Egyptian Gods. Using "Valkyrion the Magna Warrior" in combination with "Magnet Force" and predicting Atem's moves, Yugi was able to redirect the blasts from "Slifer the Sky Dragon" back at the Gods, lowering their ATK and eventually destroying them. Yugi and Atem continued to battle using cards that both of them had used before together. When Atem Summoned "Dark Magician" and "Dark Magician Girl", Yugi fought them using cards like he used against Yami Bakura and played "Gold Sarcophagus", predicting Atem would use "Monster Reborn". Once the magicians were defeated, Atem attempted to revive "Slifer the Sky Dragon" using "Monster Reborn", but Yugi revealed that he had selected that card with "Gold Sarcophagus" and negated its effect. Yugi reluctantly attacked Atem directly with "Silent Magician", winning the Duel.
With the Duel over Yugi wept. He called himself weak and said that he had always followed Atem, wanting to be as strong as him. However Atem said that Yugi has the strength of tenderness, which Yugi has also taught him. Yugi called Atem "the other me", but Atem said that he is no longer another Yugi and Yugi Muto is now himself and nobody else. (In the English version, as Yugi wept, he said that he had been so focused on the Duel, he forgot what winning meant. However Atem said that Yugi has opened the door for him, so he can finally be at rest where he belongs and that they have fulfilled their destiny. Yugi said that he was going to miss Atem, but Atem said that they will never be truly apart as the gift of kindness Yugi has given him and the kindness he has given Yugi will bind them forever.)
The Eye of Wdjat then began to glow and upon hearing Atem say his name, opened the door to the spirit world. Yugi and his friends tried to convince Atem to stay. After Joey convinced Téa that the pharaoh had to go, Yugi said that he will never forget Atem. (In the English version, Yugi said that it's like they always say "It's your move!".) Once the doorway shut, the chamber began to shake. Yugi and the others all ran outside, while the shrine collapsed, burying the Millennium Items with it.
Yugi, Joey, Téa, Tristan flew back to Japan afterwards and Yugi received a hug from Rebecca at the airport. Later when he met up with his friends again, he thought that this isn't the tale of the pharaoh; Everyone has their own story and although one has just ended, his own is just beginning.
Jaden Yuki bumps into him on the way to the Duel Academy sign ups. Yugi gives Jaden the card "Winged Kuriboh". In the Japanese version he says the card is lucky. In the English version, he says that he feels the card belongs with Jaden.Yugi's Deck goes on display at Duel Academy. Later on, it is stolen by Dimitri, who Duels Jaden with it. During the Duel, Dimitri began to mimic Yugi and a shaded figure of Yugi appeared behind him. Afterwards the Deck is returned.
In his Duel with Gravekeeper's Chief, Jaden mentioned that Yugi had won many Shadow Duels. While Lyman Banner was giving a history lesson, he mentions Yugi and Kaiba as the best Duelists of their generation and shows drawings of them to the class. One of the girls in the class says that they are one of the best looking, and another girl calls them dream boats.During Jaden's Duel with the Dark Magician Girl, Bastion Misawa and Zane Truesdale state that Yugi's the only Duelist that possesses the "Dark Magician Girl" card, making them confused about who Jaden's Dueling against.
When Jaden visits the Kame Game shop during the school trip, Solomon Muto states Yugi went on another journey and he does not know when he will come back.While Jaden is Dueling T-Bone, Jaden gives T-Bone some words of wisdom, which Solomon Muto believes to be exactly what Yugi would have said.
During Jaden's last year, the person who had gained the most graduation points at the exam would get a copy of Yugi's Deck, excluding the God Cards. Chazz Princeton, Alexis Rhodes and Syrus Truesdale qualified, but turned down the prize in favor of their own decks. During the graduation party, Jaden is led by Winged Kuriboh to the room containing Yugi's Deck. Yugi appears and sends Jaden back in time to Duel his younger self. Yugi seems to be taller and more muscular.
Yugi won Battle City V2 at some point and a had a dream where Kuriboh told him he would meet someone and have to Duel him. Shortly after this, Yugi bumped into Jaden Yuki, who had been sent back in time by Yugi's future self. Jaden showed Yugi a "Winged Kuriboh" card, which he said Yugi had given to him and it helped him come here. Yugi saw that Jaden's "Winged Kuriboh" looked like his own "Kuriboh", but had no knowledge of ever meeting Jaden or giving him a card. He told Jaden about his dream and asked if Jaden was there to Duel him.
The two proceeded to Domino City Plaza, where they saw that time had frozen and nobody else was around and began to Duel. Yugi was impressed by Jaden's "Elemental Hero" cards. After Jaden got the upper hand, Yugi switched to Yami Yugi, who Summoned "Slifer the Sky Dragon", stating that the only worthy opponent for Jaden is a god. Jaden then remembered the important thing that he had lost - how to have fun in a Duel regardless of its importance. No outcome to the Duel is shown and Jaden returned to his own time.
====Yu-Gi-Oh! 3D Bonds Beyond TimeEdit====
Yugi attended an event, where Pegasus was handing out cards to young children. Paradox time traveled to this event in order to kill Pegasus. He Summoned "Cyber End Dragon" and used it to attack and kill people, including Pegasus and Grandpa. Yugi managed to survive the attack and began to search for survivors. He then found his grandfather's bandanna and wept over his death. However the Crimson Dragon appeared and swallowed Yugi.
Yugi was taken back in time to half an hour previous, where he was joined by Yusei Fudo and Jaden Yuki, who were also time traveling. Jaden and Yusei told Yugi what they knew about Paradox and Yugi agreed to help them try and stop him. Before Paradox was able to kill the people again, Jaden got Yubel to scare them away, resulting in their running to safety. Yugi, Jaden and Yusei then confronted Paradox, who explained that he was from a future destroyed by Duel Monsters and is now trying to prevent its creation. Yugi, Jaden and Yusei dueled Paradox with a time limit of twenty minutes, by which time Pegasus would arrive. Yugi switched to Yami Yugi, who together with Jaden and Yusei won the Duel.
With everything returned to normal, as Yami, Yugi said goodbye to Jaden and Yusei before they returned to their own times and hoped to meet them again.
In this version, Yugi appears considerably taller, though he has not aged. When shown in scenes beside Yusei or Jaden, he (including his hair) is generally the same height as them, only being shorter by a very small length, though he technically should be much shorter than them. in what if episode yugi get his pizze tooking way form him and yugi did not time to put his shoes on he runs after the guy as soon yugi walks on to the beach he ends up have to duel his colne and in end yugi is defeated by his clone and yugi clone grabs yugi by the hair punchs him in the stomach the punch knocks yugi out and yugi ties yugi to chair tapes yugi motuh shut yugi clone ties the ropes super tight around yugi makeing sure he cant get free then yugi clone took his place duels rebecca he defeated her tied her up to chair next to yugi taped her motuh shut how ever yugi clone is dueled by yami later and yami beats him unties yugi and rebecca
=== . yugi moto===