Yu-Gi-Oh! is a show about a boy named Yugi Moto and his alter-ego who lives in his pendant known as the Millennium Puzzle, Yami Yugi, who plays a card game known as Duel Monsters. However, everything is not so simple. The game of Duel Monsters originates in ancient Egypt, and the monsters in the cards are based off of real monsters. Also, the Millennium Puzzle holds several powerful secrets that several people want to get their hands on.
With Dartz finally defeated, Yugi and his friends are taking a well-deserved break. However, it doesn't last long, as everyone realizes that they have no way to get back to Domino. Luckily, Mokuba arrives to say that if they participate in Kaiba Corporation’s new tournament, they will get a free ride home. Yugi, Joey, and Rebecca each receive their formal invitations and Mokuba and Roland fly the gang to Kaiba Land. There, they enter the Kaiba Dome, where there is a huge dueling arena where duelists can challenge an expert duel computer.
In the dome, Yugi and his friends meet Leon Wilson, a boy who has idolized Yugi since he won Duelist Kingdom, and Rick, a boy with an unbalanced deck consisting of mostly Dragon cards. Yugi gives him one of his Magic cards, and Rick decides to challenge the duel computer. But right when he does, a mysterious man hacks into Kaiba Corporation’s computer system and shuts and locks all the doors out of the main arena, and programs the duel computer to not open the doors unless someone defeats the duel computer. Rick has no chance to defeat the computer on its highest setting, so Yami steps in to duel, but can even the King of Games win with an unbalanced and weak deck?
Things do not look good for Yugi as the duel computer pounds his weak dragon cards to submission. Kaiba finds out about the situation and rushes to Kaiba land to help. Meanwhile, the hacker who set all this up is walking to his jet prepared to go to Kaiba land as well. Back at the duel, Yami Yugi draws the card he gave to Rick earlier, Heart of the Underdog. Using it, he is able to bring out the power of Rick's dragon deck and win the duel, causing the doors to open again. At about that time, Kaiba arrives and tells them where to register for the KC Grand Championship. That night, the gang goes to a hotel reception where all the other contestants are. There, they meet Leon again, and a duelist who seems to have a crush on Yugi named Vivian Wong. Also, the hacker arrives and introduces him to Kaiba as Zigfried Lloyd. Finally, all the contestants arrive and Roland announces their names to the crowd. Then he explains that whoever emerges as the winner of the tournament will gain the right to duel Yugi Muto for the title of the world's best duelist.
As the tournament begins, the first two duels are announced as Joey Wheeler vs. Apdnarg Otum and Leon Wilson vs. Dr. Richard Goat. Leon and Goat both arrive at their designated duel area on time, and so does Apdnarg, but Joey doesn't realize he has to be at his duel area, and because of that, must race against time to find Apdnarg in the Amazon Cruise zone. When Joey and the other eventually get there, the two start their duel. However, Yugi, Tea, and Tristan are too preoccupied by how much Apdnarg looks like Yugi's grandpa. Professor Hawkins appears behind them to fill them in. Solomon had called him to tell him that he would be participating in Kaiba's new tournament. As the duel begins, Apdnarg begins pummeling Joey with a very well-thought out strategy, while Joey attempts to improvise everything. Apdnarg soon plays his Stone Giant and his Ancient City, which special summons two Stone Giant tokens. In addition, he claims that the worst is yet to come...
As the duel between Joey and Apdnarg Otum continues, Apdnarg continues playing by his strategy, playing strange moves that don't seem to make much sense, such as switching his Stone Giant tokens into defense mode and losing 1000 life points because of it. While Joey is still being confused by Apdnarg's moves, Leon Wilson wins his duel against Richard Goat. Meanwhile, outside of Kaiba Land, Weevil Underwood and Rex Raptor arrive and plan to sneak into the KC Grand Championship to face Yugi and Joey again. Back at the duel, Apdnarg reveals that everything he is done since his first move was to summon his next monster. Using the power of his Ancient cards, Apdnarg summons the Ancient Dragon. On the sidelines, Professor Hawkins explains that without the Ancient City, Stone Giant, two Stone Giant Tokens, Ancient Key, Ancient Tome, and Ancient Gate cards, you cannot summon the Ancient Dragon. He also explains that he and Solomon had a contest to see who could collect all the cards needed to summon the dragon first. Back at the duel, though the Ancient Dragon is powerful, Joey manages to destroy it with his Gilford the Lightning, but because of its special effect, it is able to revive because Ancient City was still on the field. Joey comes up with his own strategy, and manages to destroy both the Ancient Dragon and the Ancient City, leaving Apdnarg wide open for an attack. Joey directly attacks him, winning the duel. Everyone is stunned to see Joey actually winning the duel, but not as stunned as Joey when he finds out that Apdnarg is actually Solomon Muto.
With the first match over, Rebecca is ready for her duel with Vivian. As the two rivals face off, Rebecca proves her skill by constantly turning the tide in her favor. Meanwhile, Weevil and Rex have snuck into Kaiba Land in an attempt to join the tournament. They capture Fortune Salim and steal his outfit. Back at the duel, Rebecca sticks to her strategy and defeats Vivian. As the gang watches a new duel unfold on a television screen, they are shocked to see Fortune Salim turn out to be Weevil and Rex in disguise. However, their planned opponent, Zigfried Lloyd, isn't worried about them and offers to have them both duel him at once. While Weevil and Rex both summon high-powered monsters, Zigfried plays a single Magic Card, Ride of the Valkyries, and uses it to win the duel in a single turn!
Joey's next opponent is Zigfried Lloyd, the man who defeated both Weevil and Rex in a single turn, but he is still confident he will win. As four duels simultaneous start, Zigfried begins playing with Joey's head by insulting him. This seems to work, as Zigfried quickly gains the upper hand as the duel begins. Zigfried is also worried that Kaiba may be thrown off his scent with his recent inactivity, so he activates a computer virus that causes all the attractions at Kaiba Land to go haywire. As Kaiba works furiously to fix the problem, he remembers meeting a small boy with insane hacking skills at one of his father's parties once. Back at the duel, Joey turns the tables on Zigfried by attacking him directly with his Jinzo. However, that will not last for long, as Zigfried plays his magic card Ride of the Valkyries, the same card he used to defeat Weevil and Rex.
As the duel continues, Zigfried summons his powerful Valkyrie monsters to the field to attack Joey, but Joey manages to survive the attack. Zigfried is undaunted, and plays his three Goddess sisters, Urd, Verdande, and Skuld. He also plays Nibelung's Ring on Joey's field. He uses all these cards to slowly destroy all of Joey's monsters one by one. Joey tries to turn the tables, but things look even worse as Zigfried summons his most powerful Valkyrie monster, Valkyrie Brunhilde. Joey tries to depend on luck but each turn Zigfried takes away one monster and is able to see his cards!
The final four duelists have been chosen: Zigfried Lloyd, Leon Wilson, Rebecca Hawkins, and Balfry Ginger. As Yugi and the others prepare to cheer Rebecca on in her next duel against Leon, Professor Hawkins appears and informs the group that Yugi's grandpa has disappeared! Arthur heads off to cheer Rebecca on while Yugi and the rest while Yugi and the others go searching for Solomon. They eventually find a map that they think will lead them to him, but Duke suspects a trap. Meanwhile, Rebecca and Leon begin their duel. Rebecca tries to start the same strategy she used against Vivian, but Leon turns out to be too good an opponent to be trapped by that as he foils her attempts to get her strategy started. Then he begins playing many fairy tale monsters against Rebecca. Rebecca is surprised that Leon would have a deck like this, and even more surprised that she is being defeated by it. Meanwhile, Zigfried wins his duel against Balfry Ginger, meaning he gets to be in the finals. Finally, Yugi and the others arrive at the Chinese restaurant where they think Yugi's grandpa is being held.
As Yugi and his friends enter the restaurant, they find Vivian and Yugi's grandpa. Solomon explains how Vivian helped cure his back pain, but then Vivian undoes what she did earlier, bringing his back pain back. She challenges Yugi to a duel for his grandpa and Yugi accepts. Yugi duels Vivian and wins without much of a struggle. Back at the main duel, Leon and Rebecca continue. Rebecca does manage to get the upper hand on Leon by summoning her Diamond Head Dragon. As Yugi and the others finally arrive at her duel, Leon summons his Thorn Princess card to control Rebecca's dragon and attack her life points directly with it, bringing them down to 0. Though Rebecca loses, she congratulates Leon and wishes him luck in the finals.
With Zigfried and Leon ready to square off in the KC Grand Championship finals, Kaiba appears and announces that the match is invalid and proclaims Leon Wilson to be the winner of the duel. Then he tells Zigfried that he knows that his true identity is Zigfried Von Schroeder, CEO and President of Schroeder Corp and challenges him to a duel. As Kaiba and Zigfried begin their duel, Zigfried starts off by playing his magic card Ride of the Valkyries on his first turn. Throughout the rest of the duel, he continues to pummel Kaiba with his Valkyrie monsters, but Kaiba remains unaffected and counters all of Zigfried's main offenses. However, things begin to turn in Zigfried's favor, as he plays Nibelung's Ring on Kaiba's XYZ Dragon Cannon and then plays Fortune Chariot, which lets him bypass Kaiba's monsters and directly attack him.
As Kaiba and Zigfried's duel continues, Zigfried attacks Kaiba repeatedly with his Valkyries and his monster-destroying Goddess combo. Soon Zigfried tells Kaiba why he is infiltrated Kaiba's tournament. A few years ago, Zigfried developed a holographic image projection system that could be used on Duel Monsters cards. However, Kaiba had developed the same idea at the same time and beat Zigfried to it by making a deal with Pegasus. Now Zigfried is back for revenge. Kaiba is unaffected by Zigfried's story and continues dueling, summoning his Chaos Emperor Dragon and destroys everything. However, Zigfried is able to quickly bring back his Valkyrie Brunhilde. However, through a very complicated combo, Kaiba is able to revive his three Blue Eyes White Dragons, his Chaos Emperor Dragon, and his Luster Dragon #2 all at the same time. Kaiba uses them to destroy Zigfried's Valkyrie Brunhilde and wipe out the rest of his life points.
With Kaiba's hacker trouble out of the way, it is time for the promised event: Yugi, the King of Games vs. Leon. However, things do not seem as peaceful as they are supposed to be. As Leon progresses up the stairs to the final duel of the event, Zigfried catches his eye and hands him a card with a picture of a golden castle on it, saying it will prove useful. Taking it, Leon begins his awaited duel. However, during the duel, one of Kaiba's men comes up and gives Kaiba some news that unsettles everyone present: Leon and Zigfried are brothers! However, Leon is dueling to help his brother fulfill their mission: destroy Kaiba Corp and advertise their own company.
Zigfried does not seem content with just his brother's victory in this duel. To ensure things go that way, the card he gave to Leon, The Golden Castle of Stromburg, an illegal card, has been modified to force the duelist's monsters to battle and cause Yugi's own creatures to self-destruct while Leon's remain untouched. In addition, to make things worse, Yugi has to put half his deck in the graveyard to keep it going, much to his distaste. Add to the fact that so long as the card does remain active, Kaiba's computer mainframe will be infected with an unstoppable virus, and you have a recipe for the ultimate disaster. Even Leon isn't happy with the arrangement, especially since it's cheating. However, Leon's pleas fall on Zigfried's deaf ears as he controls the duel from the balcony. However, Yugi promises that he'll help Leon destroy the castle somehow. But how can he destroy a card that can't be affected by traps and spells?
Yugi continues his duel with Leon, who is using the Golden Castle of Stromberg card that Zigfried gave to him. Leon wants to get rid of the card because its affects and how Zigfried was only helping him cheat. Yugi puts together a strategy to get rid of it by summoning Jack's Knight, Queen's Knight, and king's knight. Then he used a magic card that sacrificed all three monsters in order to summon Royal Card Knight. By discarding a monster, each of the first five levels, the knight can destroy every card on the field, but when the smoke clears it turns out the castle is also immune to monster special abilities as well. But then Yugi points out that because he only has one card in his deck, he can't discard half of his deck to keep the castle on the field, therefore, the castle is ruined. Leon doesn’t want to finish because he felt liked he cheated but Yugi convinces him to continue, and with one card left, Yugi summons Dark Magician and uses Diffusion Wave Motion to destroy all of Leon’s monsters and wipe out his life points. Yugi won the tournament and he hoped to see Leon again so they can duel fair. Afterwards, Yugi and his friends left by private plane to go back home where Yugi hopes to finally recover the pharaoh’s memories.
Mr. Muto tells his grandson the story of how he received the Millennium Puzzle and how a mysterious man saved him after one of his guides betrayed him. During the night, Rex and Weevil break into Yugi's room and steal his duffle bag to get the three Egyptian cards. Yugi wakes up from the noise and chases them out into the street. They're surprised to find the Millennium Items inside the bag. When Yugi finally catches up with them, he ends up face-to-face with Yami Bakura.
Dark Bakura kidnaps Mokuba and forces Kaiba to duel him. Planning to claim the power of the Blue-Eyes as his own, Bakura attacks using a new deck of Egyptian-themed cards, including his spirit beast, Diabound. Diabound is able to absorb some of the power of the Blue-Eyes, and Bakura abandons the duel. However, he leaves a parting gift for Kaiba - the Millennium Eye.
The Pharaoh, Yugi, Tea, Joey and Tristan arrive in Egypt and meet up with Marik. The Pharaoh presents the Egyptian God cards to the stone tablet and his spirit is sent five thousand years into the past to when he was still alive and reigned as King of Egypt. Little does he know, Bakura has followed him, intending to finish the battle he started thousands of years ago.
Bakura's ancient alter ego, the Thief King, arrives at the palace to claim the Millennium Items for himself. The priests engage him in battle, but Bakura's spirit beast Diabound proves too much for them to handle, until the Pharaoh steps in and summons Obelisk the Tormentor. Meanwhile, the spirits of Yugi and the others enter the Millennium Puzzle in search of a doorway into the Pharaoh's memories.
Bakura's Diabound fights against the Pharaoh's Obelisk, but their power is equal, and Bakura is forced to retreat. Mana, a magician and also a childhood friend of the Pharaoh's, arrives to visit the palace. Mahad decides to help protect the former Pharaoh's tomb, despite Isis' visions of his fate.
Mahad unlocks his full power using the Millennium Ring, and forces Bakura to face him by trapping them both inside the tomb. Mahad's Illusion Magician faces off against Bakura's Diabound, which has grown in strength since his battle with the Pharaoh. Diabound gains the upper hand, and Bakura finishes the job by deliberately setting off the tomb's traps. To save himself, Mahad fuses his soul with his spirit beast, the Illusion Magician, transforming himself into the Dark Magician. Bakura takes the Millennium Ring and escapes, while Mahad's soul is sealed into the stone tablet meant for Diabound.
Mana is distraught at the loss of her master. Isis explains that he has become the Dark Magician and will eventually return with greater powers then ever before. Seto and Shada head out into the city to search for people with strong spirit beasts. Seto meets a girl named Kisara who is shunned by the citizens because of her strange white skin and blue eyes. Meanwhile, Yugi and the others find the doorway into the memory world and begin searching for the Pharaoh.
Bakura breaks into the palace again and attacks Akunadin, infusing part of his evil soul into the Millennium Eye. The Pharaoh summons Slifer the Sky Dragon to chase after Bakura and Diabound. When Bakura begins targeting the villagers, Slifer is forced to take Diabound's attacks in order to defend the helpless people. The wounded Akunadin reminisces about the creation of the Millennium Items through the destruction of Kul Elna, and how he was forced to abandon his own son, Seto.
Seto and Kalim arrive to defend the Pharaoh. Bakura pretends to retreat and leads them into a trap, giving him the chance to finally defeat Slifer. Yugi and the others appear just in time, giving the Pharaoh the strength he needs to summon the Winged Dragon of Ra. However, Bakura uses Zorc's power to turn back time so he can make sure Yugi never shows up. The Pharaoh is defeated and Bakura takes the Millennium Puzzle.
Akunadin forces Kisara to fight the other prisoners in an attempt to force her to call forth her spirit beast. Despite Akunadin urging him not to, Seto steps in to protect Kisara until she is finally able to summon the Blue-Eyes White Dragon. Meanwhile, Yugi and the gang search for the Pharaoh, who they firmly believe to be still alive. During their search, they run into Mana, who decides to help them. They find the Pharaoh taking shelter in a cave, though he is badly injured.
The priests meet up with the Pharaoh and the others, and together they track Bakura to Kul Elna, a ruined village haunted by the vengeful spirits of its former people. The Pharaoh heads in to face Bakura alone, but is soon joined by the spirit of Mahad, in the form of the Dark Magician. Bakura summons Diabound, newly evolved after its battle with Slifer, to combat him. Mana finally unlocks the power of her spirit beast, the Dark Magician Girl, and rushes to their aid.
Mahad and Mana mount a counterattack on Diabound, but he absorbs the dead spirits of Kul Elna to make himself even more powerful. Seto and the rest of the priests arrive to fight him, but they are unable to penatrate his spirit shield. Bakura takes the Millennium Scale from Kalim and uses it to strengthen Diabound even more. Shada locates Diabound's stone tablet, and plans to destroy it to eliminate the beast. However, Akunadin attacks him and takes the Millennium Key.
Yugi and the others enter the palace to search for clues about the Pharaoh's real name. Mahad is finally able to defeat Diabound, with help from the former Pharaoh, and Bakura's physical body is destroyed. However, Akunadin betrays the priests, taking the Millennium Items, giving him the power to resurrect the Dark God Zorc from the Millennium Stone. Akunadin is reborn as the High Priest of Darkness. Bakura reveals the true nature of the Shadow Game - it is simply a board game, played by the present-day versions of Dark Bakura and the Pharaoh.
Kaiba arrives in Egypt. Ishizu and Marik lead him to the stone tablet shrine, where the Millennium Eye begins glowing and shows his visions of Bakura and the Pharaoh's Shadow Game. Bakura pulls his soul into the game and uses it to help resurrect the Thief King. Meanwhile, Bobasa guides Yugi and the others to the Valley of the Kings, where the Pharaoh's true name lies within his future tomb.
Bakura revives Diabound, stronger than ever thanks to the Millennium Items. To give Zorc enough time to fully be reborn, he separates the Pharaoh and his priests from one another, and attacks them with armies of monsters while they are isolated. Kalim is killed, but not before giving his remaining power to Shada. The Pharaoh heads back to the palace to find Seto.
Seto and Kisara face Akunadin, however Kisara is killed and the White Dragon is sealed in stone. The Pharaoh makes it back to the palace, however he is forced to engage battle against Seto, since his mind is manipulated by the evil mage Akunadin. The legendary ancient match between the Pharaoh and Priest Seto begins. The Pharaoh summons Mahad to fight against the Blue-Eyes White Dragon, now controllled by Seto.
Thief Bakura succeeds in reviving Zorc Necrophades, sacrificing himself and his Diabound in the process and scattering the Millennium Items throughout Kul Elna. Meanwhile, Yugi and Dark Bakura duel. If Yugi wins, he can leave and tell the Pharaoh his true name, and if he loses, he'll never leave. Meanwhile, the Pharaoh and Kaiba talk about events that happened in the previous episode. The Pharaoh and Seto ride back to the palace and attempt to stop Zorc. Shada is killed by a lightning bolt.
Isis and Mana head for Kul Elna to retrieve the Millennium Items. The duel between Yugi and Bakura continues. Once Mana delivers the Millennium Items to Shamon, Shamon summons Exodia, which holds its own against Zorc, until Zorc eventually overpowers it and destroys it, killing Shamon. Mana delivers the other Items to the Pharaoh and the Pharaoh prepares to fight Zorc.
The Pharaoh summons the Three Egyptian Gods to combat Zorc. Meanwhile, at the tabletop, Bakura claims that he'll return to his original form and both leave the table and join with their 3000-year old counterparts. Zorc defeats the Gods by covering the sun, wiping their strength out.
Mana takes the Pharaoh back to the palace while Seto summons Blue-Eyes White Dragon to combat Zorc. Blue-Eyes White Dragon stops the solar eclipse, but is defeated by Zorc, submitting to darkness. Kaiba takes over and summons Blue-Eyes Ultimate Dragon, which is equal to Zorc. Meanwhile, Yugi successfully defeats Dark Bakura with Gandora, the Dragon of Destruction. The Pharaoh becomes Black Luster Soldier and fuses with Blue-Eyes Ultimate Dragon, becoming Master of Dragon Knight. Master of Dragon Knight is destroyed by its own attack and the Pharaoh is seemingly defeated, but Yugi and his friends fly to him.
The Pharaoh continues his battle between Zorc in the Memory World. Yugi, Joey, and others summon monsters, such as the Dark Magician, to help the Pharaoh. The ancient characters cannot be read but Yugi is going to reveal the Pharaoh's true name. Tea then remembers the cartouche pendant and passes it to the Pharaoh. The Pharaoh regained his true name, "Atem", the keyword which allowed him to summon the three Egyptian Gods and fuse them together to form the Creator of Light. Zorc was defeated.
Atem and the others return to present-day Egypt. Atem has set his mind to sealing the seven Millennium Items with himself. Someone must be able to defeat Atem in a duel to do so. Although Kaiba and Joey both volunteer, it will be Yugi that will take the honor. The duel will take place tomorrow, and both Pharaoh Atem and Yugi construct the best deck possible to each of their abilities.
Yugi and Atem place the seven Millennium Items into their slots in the Pharaoh's Memory in the shrine of the Underworld. Pharaoh Atem and Yugi then separate into two physical beings. The duel that will determine the fate of Atem and Yugi begin. Pharaoh Atem summons "The Tricky" with an attack power of 2000 but Yugi plays the magic card, "Swords of Revealing Light" Yugi is able to fuse the three monsters: "Green Gadget", "Red Gadget", and "Yellow Gadget" into one monster with 3000 attack points the "Mobile Fortress Stronghold".
The duel between Yugi and Atem continues. Atem summons the three gods: Ra, Obelisk and Slifer to the field. The sum of their attack power exceeds ten thousand. Yugi is overwhelmed, but he parries Slifer's Summon Thunder Bullet with this episode's Key Point: a Quick Magic card, "Mirage Magic." When a player's monsters' Attack Power and Defense Power increase or decrease due to an opponent's card, this negates the effect and recovers the difference in Life Points. Furthermore, Yugi also dodges Obelisk's attack with the Trap card "Mirage Ruler." Yugi finally makes a counterattack move that threatens the gods.
Yugi is successful in defeating the Egyptian Gods. However, Atem is not worried at all. Atem admits that he knew that Yugi would defeat the Egyptian Gods. Now the real duel begins between Yugi and Atem. Now, Yugi must face his most trusted creature, the Dark Magician, if he wants to help Atem. (Note: When this aired in the U.S, the ending said "To Be Concluded" instead of "To Be Continued", thus signifying the end of the series.)
Yugi tries his best to fend off the attacks from Atem's most powerful trump card the "Dark Magician." Yugi then plays his Spell Card, "Golden Chest of Sealing." The power of the Golden Chest of Sealing is it can negate the effects of another magic card that is stored in the chest. Yugi was finally able to defeat the "Dark Magician" with his "Silent Magician." Atem tries to activate the Spell card Monster Reborn so he can revive Slifer the Sky Dragon, but when Yugi opens the Golden Chest of Sealing to reveal the card he sealed, the card was "Monster Reborn". It means neither of them can use that card in this game. It is Yugi's message to another Yugi that "Those of the dead should not remain in the world of the living."