The story begins in Ancient Egypt, with the prince of the dynasty (Atem), who often spends time at the dueling ground playing against other villagers, and his two friends, Jono and Teana. One night, Atem escapes Simon Muran, his tutor and advisor, to visit the dueling grounds, where he mets up with Tea and a few villagers. After some games, Tea tells him of a festival occurring in the Plaza, and they leave to see it. They watch the mages march around a shrine, holding flags, and Tea comments that the ceremonies are starting to seem darker, assuming that it is the work of the "detestable" high mage Heishin, a sorcerer who leads a group of independent high mages. Teana spots Jono dueling, and greets him just as Jono's opponent, Priest Seto, defeats him. Priest Seto mocks Jono's ineptitude in dueling, and Jono and Teana tell Seto that Atem could easily defeat him. Seto and Atem are about to duel when one of Heishin's aides tells Seto that Heishin requests his presence. Seto agrees to duel Atem later at the dueling grounds. Jono, Teana, and Atem return to the grounds, where Atem has a quick duel with Jono and defeats him. Seto returns, flanked by aides, and duels Atem, putting on quite a display of ability before Atem claims victory. Seto recognizes that Atem is the prince (note that none of his dueling friends have ever realized this) and says he will meet Atem again. Atem leaves and returns to the palace and is herded off to bed by Simon Muran. As Muran walks away, a guard tells Muran that Heishin has invaded the palace, wielding some sort of strange magic. Muran starts looking for him and finds Heishin destroying the stone columns of a walkway. Heishin confronts Muran and tells him that he has discovered the Dark Power, and uses the Millennium Rod (or a staff that looks almost exactly like it) to blast Muran away. Meanwhile, the Queen wakes Atem and tells him to run, just as Priest Seto captures her and his aides take her away. Seto tells Atem that Heishin holds the King and Queen captive, and that to run away would result in their execution. Seto then demands the Millennium Puzzle in exchange for a getaway. Atem refuses, and Muran runs up behind him, looking beaten and weak, carrying the Puzzle and telling him to run. Atem runs, but Heishin corners him, and forces him to duel for the fate of the Puzzle. However, Heishin defeats Atem (the player will continue to duel Heishin until he or she loses), and Muran tells Atem to shatter the Puzzle, even attempting to subdue Heishin. Atem smashes it against a wall, and Muran uses some magic to seal himself and Atem into the puzzle. Muran tells him that Atem's soul is now locked inside the puzzle, and that the only way to release it is to reassemble it. Muran tells Atem to rest, assuring him that someone will eventually complete it.
A millennnia later the puzzle is solved by Yugi Moto. Yugi has a dream about the Puzzle's contents before entering a Duel Monsters Tournament hosted by the Kaiba Corporation. After defeating the preliminary rounds by dueling and defeating Rex Raptor, Weevil Underwood, Mai Valentine, and Bandit Keith (in that order), he takes a break. Between the preliminaries and the finals, Yugi and Joey are talking when Yugi spots Shadi, and tells Shadi about the dream. Shadi suggests that Yugi meet Atem through his Millennium Key, and transports Yugi into the Puzzle. Yugi meets Atem, and Atem mentally tells Yugi that he wants to return to his own world. Atem gives Yugi six blank cards and disappears. After waking Shadi asks what happened, and Yugi shows him the cards, but neither of them can deduce what their purpose is. Joey informs Yugi that the finals are about to begin, and they depart. The first finalist is Shadi, and after Yugi defeats him, the Millennium Key and Scales are forced into the blank cards. Shadi theorizes that the Millennium items were drawn together so that Yugi could acquire all of them. Yugi then proceeds to defeat Bakura, Pegasus, and Isis (Ishizu) to acquire their items. In the last round of the finals, Yugi faces Kaiba, who, oddly enough, possess the Millennium Rod. Yugi defeats Kaiba and unites all of the Items, which allows Atem to travel into his Egyptian past.
Shimon Muran awakes Atem in the puzzle, and theorizes that the boy, Yugi, is a representation of the future of Atem. Muran then tells Atem of the current situation. Heishin and the High Mages have taken control of six of the Millennium Items, and rules over the Metropolis. He expands his kingdom by constructing shrines guarded by the five High Mages: Martis, Secmeton, Atenza, Kepura, and Anubisius. Each shrine contains one of the Items, while the Millennium Rod is guarded by Heishin and Seto. Muran warns Atem that the way to defeat them is to find the Forbidden Ruins, and passes away. Atem is transported back to the Shrine of Glory, which is abandoned. He then travels into the old city, now known as the Metropolis, and ventures into the old dueling grounds, which are destroyed. Jono sees him and is jubilant that he survived, and brings him back to the new dueling ground, where he is re-united with Teana and the other villagers, who are hiding underground. Jono tells Atem how the Mages destroyed the card shop and dueling grounds because the villages couldn't locate him. Everyone is relived that Atem survived, and Jono briefs Atem on the political situation, and how the Mages, led by Heishin, govern the land from the Vast Shrine of Darkness. Atem leaves and visits the old palace, which is completely destroyed. He meets a soldier inside, who Atem defeats in a duel and starts searching the room. He finds a map that depicts an area known as the Forbidden Ruins. He travels to the Valley of the Kings, where he meets Sadin, a tomb-keeper who is related to Shadi. Sadin takes the map and directs him to the Forbidden Ruins, where Sadin points out a map and drawing on opposite walls. After viewing the drawing and ascertaining nothing, Atem looks at the Map while Seto sneaks up behind them and tells them that the Map reveals the location of the High Mages and the Millennium Items. After Seto urges Atem to defeat the High Mages, Sadin yells at him to leave and advises Atem to proceed with caution, since Seto is an enemy and any positive action on Seto's part could be equally dangerous.
Atem defeats High Mages Martis of the Desert Shrine (who duels on a Wasteland terrain) and takes the item he guards. Atem then defeats High Mage Atenza (who duels on a Mountain terrain) and captures his Item. He decides to take a break at the Hidden Dueling Grounds, and discovers that Teana was kidnapped by Seto. Atem and Jono head to the Dark Shrine, which is unguarded, and storm the building to discover a labyrinth guarded by a Mage. Atem duels and defeats him, and tries to navigate the labyrinth, only to constantly open the wrong doors and duel more mages (at which point Jono says "Y'know...I think we're lost"). Atem finally finds the correct door, and finds Seto and Heishin with some aides, holding down Teana. Heishin briefly contemplates the existence of the Prince and the Puzzle, and commands Seto to duel Atem and secure the Puzzle, which would be Seto's reward for victory. Seto drags Teana into a secret room and duels Atem, using incredibly strong monsters (with attack powers of 3000+) and strong magic cards before finally losing to Atem for the 2nd time. Seto gloats, stating that the High Mages won't stand a chance against Atem and departs. Teana thanks Jono and Atem for the rescue, and as they travel back to the Hidden Dueling Grounds, wonders why Seto was gloating after his loss, remarking that he "seemed to have a different agenda", while Jono tells Atem to be cautious as they part ways. Atem finds and defeats High Mages Secmeton, Kepura, and Anubisius to gain a total of 6 out of 7 Millennium Items. Seto then sneaks up behind Atem again and tells him to defeat Heishin by accessing the now unguarded Dark Shrine. After returning to the Hidden Dueling Grounds, the villagers and Jono and Teana congratulate Atem on his victories and hope for a better future.
He then heads for the Dark Shrine located north of the dynasty. Seto shows up in the grand hall, and shows Atem a hidden door that leads directly to Heishin's throne. Seto also warns Atem that Heishin is guarded by mages who have sworn to defend Heishin to the death. Atem passes through the door and is accosted by Neku and Sebek, whom he duels and defeats on a Darkness terrain. Finally, Heishin enters and climatically duels Atem for the second time, playing on a Darkness terrain with cards with attack powers of 3500-3750. Atem overwhelms him and Heishin is promptly knocked unconscious. Seto enters the room brandishing the Millennium Rod, stating that all of the Items have been gathered in one place, and should be brought to the Forbidden Ruins. Seto finally reveals his hand, stating that he only encouraged Atem to gather the items to save Seto the trouble of doing it himself. Seto then pushes a false stone, revealing a hidden chamber with a statue with the Darknite. Seto then challenges Atem a duel, each betting their collection of Items. Seto initially gains a lead with his multiple Blue-Eyes Ultimate Dragons, Gate Guardians, and Meteor Black Dragons, but Atem eventually defeats him. Just as Atem is about to decide whether or not to keep or destroy the Items, Heishin appears, grabs Seto, and motions a sword at his neck, threatening to kill Seto if Atem fails to hand over the Items. Atem reluctantly gives them to Heishin, who places them in the statue, causing the Darknite to be summoned. Heishin commands Darknite to obey, but the Darknite refuses, and since Heishin lacked the Item to prove his authority, Darknite locks him in a card and incinerates him. Just as Darknite is about to do the same with Seto and Atem, Atem shows Darknite the card Yugi used to acquire the Millennium Items, proving that they had them (or did at one point). Darknite agrees to duel Atem for his survival, under the conditions that Darknite depart if Atem wins. Atem defeats Darknite's monsters and superior spells and traps quickly, but Darknite does not uphold his end of the deal and transforms into Nitemare. Nitemare challenges Atem to another duel, and uses a combination of Seto's excellent monsters and Darknite' superior spells and traps. After a long and harrowing duel, Nitemare is finally defeated. Seto escapes and is never seen again. Atem orders the Forbidden Ruins buried, and claims the rightful throne, leading his kingdom for thousands of peaceful and prosperous years.
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