The Dark Side Of Dimensions
In Kul Elna, the Shrine of the Underworld is excavated by KaibaCorp, with Mani, among the workers. One of the other workers takes out a device, displaying an image of the Millennium Puzzle being worn by Yugi Muto, so that he knows what it is they are looking for. He exits the shrine just as a helicopter, carrying Mokuba Kaiba flies past.

At Kame Game, Yugi is leaving to go to school, but is stopped by Solomon Muto, who comments on Téa Gardner. Yugi leaves and at a flight of stairs, meets Téa, who greets him with a shoulder bump.

Joey Wheeler hurriedly cycles to school. His carelessness causes him to get soaked by Sanpei emptying a bucket of water and knock over a policeman. Yugi and Téa arrive at school, where they spot Ryo Bakura, who is being obsessed over by a group of girls. Joey catches up with Tristan Taylor and with one minute before the school gate closes, Tristan gets onto the back of Joey's bike. The two speed downhill and get inside the gate, just as Mr. Karita shuts it.

At lunchtime on the roof of the school, Yugi and his friends discuss their futures. Téa has been accepted for a study abroad program and wishes to become a professional dancer. Tristan is unhappy with the job he has lined up working in his father's factory. Joey would like to become a professional Duelist and claims there is no one out there who can stop him, but Tristan points out that their math teacher can, having confiscated Joey's Duel Disk for polishing it in class. Téa encourages Yugi to tell the group his plan. He reckons he will stay working in Kame Game, helping his grandfather, but also intends to design on his own games, hoping that one day he will invent one that they can all play together. Joey proposes a pact that they all meet up to play Yugi's game, after it makes it big. Yugi is worried that they're getting overly faithful of his success, but Téa assures him that he can do it.

When Yugi and his friends return to class, they spot a new student. They think that they remember him, but struggle to think of his name, before Tristan finally says that it is Aigami.

After school, Yugi is walking with Joey and Téa. Joey has his Duel Disk back. As Yugi looks through his Deck, he thinks of Atem and pauses. Joey asks him what is wrong and although Yugi insists it is nothing, Joey realizes he is thinking of Atem and say that it is impossible to forget him. Yugi reflects on the Ceremonial Battle, remembering himself sealing "Monster Reborn" in "Gold Sarcophagus", Atem walking through the Doorway to the Underworld and the Millennium Items falling into the depths of the Earth.

Joey notices Aigami, being harassed by Scud and his gang, with Scud commenting on Aigami's cute face and making provocative remarks. Joey jumps down from the bridge and approaches the group. Scud and his companions let the matter drop for the time being and leave Aigami alone, but Scud instructs Aigami to meet him at the KaibaCorp construction site later and threatens him, should he not show up. Aigami thanks Joey, Téa and Yugi and insists that he is fine, before leaving.

Later at the construction site, Scud and his gang have a video camera to record Aigami. They threaten him with various weapons and say that today's lesson is "pain". Aigami is silent at first, but laughs and asks the gang how long he has been in their memories and if they are aware that he has altered them. He produces the Quantum Cube and the lights go out. A group of children with glowing eyes appear and surround the gang. The gangsters start to glow and a symbol appears on Aigami's forehead. Scud and his gang are disintegrated and drop their camera. Aigami walks away, but returns to collect the camera.

At a church-like setting, Yami Yugi, dressed as he was while sharing Yugi's body but with two additional gold armbands, walks through a set of doors to face Kaiba. The two engage in a Duel, which ultimately ends in Kaiba's victory.

The Duel is revealed to have taken place in a virtual reality, while Kaiba is in his space station. One of Kaiba's scientists hands him a bottle of water and comments on how well the system is performing, but Kaiba is not happy. He deems the Duel imperfect, because despite the accuracy and fine-tuning of his recreation of Atem, it was not the real thing. In frustration, he throws the bottle on to the ground. Mokuba contacted the space station and informed Kaiba that they had found the pieces of the Millennium Puzzle at the excavation.

At a mall, Yugi, Téa, Tristan and Bakura are sitting at Devlin's cafe, being served by Duke Devlin, Yugi reads the news about Scud and his gang's disappearance. Yugi, Téa and Duke note that it is only one of many recent cases of people mysteriously disappearing. Bakura mentions how the person responsible could be watching them, but Anzu accredited that paranoia to the Bakura fanclub, who were spying on him from behind a pillar. Nearby, Joey is wearing a dog costume, walking around, handing out balloons. Tristan repairs Joey's Duel Disk at the table, which Duke remarks is brave of him, as he could get blamed for breaking it.

Aigami teleports to the mall, where he stands on a higher level and watches over Yugi and his friends. He reflects on the time he was in Prana Realm, a plateau above the clouds. There were seven pillars on the plateau, each depicting a Millennium Item. As Aigami stands before one of the pillars, children appear and disappear, while he and Sera remain constantly present.

Aigami reflects further back to when he and Sera were alone and thirsty in Egypt. Sera refers to Aigami as "Diva", as she gives him a cup of water. Aigami decides to leave the plateau and is followed by some of the others, including Mani.

In the present, Mani calls Aigami a few times, at the mall, before Aigami takes notice. He tries to talk him out of a revenge he knows he is considering, stating it not the target's fault or what their mentor would have wanted. He then informs him that Kaiba found the Millennium Puzzle, prompting Aigami to teleport away.

Kaiba suddenly appears on screens across the mall and introduces his new Duel Disk, which he says will be demonstrated in an exhibition Duel at Kaiba Land. Joey groans that he will not be able to afford the new Duel Disk and Tristan suggests that he will need to get another part-time job. Annoyed, Joey accuses Tristan of breaking his Duel Disk, despite having asked him to fix it, and insists that Tristan now owes him for it. The two get into a fight and their antics cause a girl to lose a balloon that Joey handed out. Téa tries to break them up, but Joey eats her ice cream, while continuing to fight. Joey's boss, Mr. Clown, sees this and lectures Joey on the importance of his job.

In Kul Elna, Mokuba and Roland are waiting for Kaiba, who soon arrives in his Blue-Eyes White Dragon jet. The group entered the Shrine of the Underworld and Kaiba notes the location of the Ceremonial Battle. He and Mokuba walk towards the disassembled Millennium Puzzle, whose pieces are being scanned by a computer. Mokuba asks how Kaiba plans on reconstructing the puzzle, when it took Yugi eight years to do so and Kaiba makes a reply about Yugi being a child when he did it.

Kaiba is informed that it takes 30 minutes to disable the security system for the Millennium Puzzle's lock. To pass the time, Kaiba says he shall have a Duel and, aware of Aigami's presence among the crowd, Kaiba calls him out, using the name, "Diva". Aigami is impressed that Kaiba knows his real name and Kaiba asks how he is in Egypt, having been in Domino City just minutes ago, while showing footage of him.

One of the KaibaCorp men threatens Aigami with a gun. An act which is mocked by Aigami, before using the Quantum Cube to make the man disappear. After witnessing this, groups of workers run away, leaving just Kaiba, Mokuba, Aigami, Mani and some KaibaCorp employees.

Aigami attempts to use his cube on Kaiba, but Kaiba readies his Duel Disk, which counters the effect of the cube. Kaiba yells, asking if Aigami thinks he can defeat him with his own power. Aigami instead challenges Kaiba to a Duel, which he accepts and the cube transforms into a Duel Disk.

Kaiba and Aigami Duel using the Dimension Area ruleset. Kaiba is outperformed at first, but resolves that he cannot lose, since he must face "Yugi", before correcting himself and saying "Atem". Kaiba slams his hand into the ground and then draws "Obelisk the Tormentor". He Summons it, which Aigami thought would be impossible, since "Obelisk" was one of the pharaoh's monsters. Kaiba sacrificed two of his monsters to use the effect of "Obelisk", leaving Aigami with 1000 Life Points.

The Duel is interrupted, as the computer finishes scanning the pieces of the Millennium Puzzle. Mokuba then hooks the case containing the puzzle to the KaibaCorp helicopter and flies away, taunting Aigami. However, Aigami teleports up onto the case and with a glowing purple hand, reaches through the glass. Mokuba sees what Aigami is doing and headbutts him, knocking him off the case. Kaiba concludes that he has what he needs and gets back into his jet to leave.

Mani notices the pit that the puzzle had been extracted from is glowing, so he teleports into it and finds the Millennium Ring.

In a dream, Joey is on the top of a flying KaibaCorp blimp, where Kaiba is patronizingly towering over him. He taunts him about the new Duel Disk, saying that a commoner like him will never be able to afford it and teasingly asks if he wants it. Joey falls off the blimp, but awakes to the school's graduation rehearsal, falling out of his chair.

On the stage, Yugi practices his speech, while Aigami stands at the back of the hall, only visible to Sera, who has just arrived. She refers to Aigami as "brother" and asks if he fought Kaiba. Aigami hands her a piece of the Millennium Puzzle that he managed to swipe, and instructs her to keep it safe. He comments on the resurrection of the pharaoh, but Sera is not too enthusiastic. She disappears, leaving Aigami to approach Yugi and his friends, expressing interest in getting to know them better.

The group go bowling with Aigami and then head to a fast-food restaurant. The group tell Aigami stories about their adventures, Joey shows his Deck to Aigami and praises Yugi's Dueling skills. Aigami shows interest in Dueling Yugi, but Joey says that he will have to get through him first, so Yugi invites them to have a Duel tournament at his house.

Kaiba enters an elevator, which takes him to the space station. He takes the Millennium Puzzle pieces to a small room and puts them on a floor, where a computer begins to put the pieces together. It provides a six-hour estimate for completion and Kaiba thinks to himself "Wait for me... Yugi".

Aigami, Bakura and Joey are on their way to visit Yugi, for the friendly tournament. Aigami shows Joey and Bakura his Quantum Cube, which he says is a Deck case, which was given to him by somebody important to him. Bakura mentions having once had an item that his father brought back from Egypt and Aigami replies that he would like to hear more of this story.

At Kame Game, Yugi is preparing his Deck for the Duel tournament, when Sera enters the store. She notices the Millennium Puzzle box, which Yugi had been keeping his cards in and comments that is pretty. Yugi tidies it away and informs her that it is not for sale.

Sera shows him the Prana Realm with the seven pillars and then takes him back to the store. She has now disappeared, but Yugi opens the puzzle box and finds the piece of the Millennium Puzzle that Aigami had given to Sera.

At the space station, the computer has almost finished reassembling the Millennium Puzzle, but reports that two pieces are missing. At first, Kaiba says that this is impossible, but then realizes that Aigami must have taken them when he put his hand through the glass.

Bakura talks about how he stowed away in the cargo of a ship in Egypt when he was young, while his father searched for the Millennium Ring, but he stops talking, unsure why he is sharing this information. Aigami uses his powers on Bakura, who cries out that he does not want to remember. A group of Plana children appear and Joey tries to get himself and Bakura to leave. Aigami sends Joey to another dimension, where he finds himself in a street, with other people walking past him. Aigami explains that this world is being sustained by Joey's memories, and that as soon as Joey forgets something it will disappear. Joey seems to take advantage of this and recreates a street he rides his bicycle down at the beginning of the movie, complete with Sanpei splashing a bucket of water on him like before. However, the people he recreated pay no attention to him. Aigami asks if Joey really thinks he can win a battle of wits with him, and decides to start erasing Joey's memories, causing the world to rapidly dissolve around him.

While Yugi is wondering where everyone is, Tristan arrives and informs him that he has found Joey's bicycle and Duel Disk abandoned, something Joey would never do. He takes Yugi on his motorbike to search for Joey and they meet with Téa.

Aigami approaches Bakura, who is cringed on the ground, in a panic. Aigami laughs and asks if he does not remember. He conjures a flashback, in which Shadi Shin is with a group of children, including Aigami, Sera and Mani. The Tablet of the Pharaoh's Memories is nearby, with the Millennium Ring and Scales inside it. Shadi explains that three of the Millennium Items are weak to evil, three represent justice and that the Millennium Puzzle contains both justice and evil. He says to Aigami that he is on the same level as the person destined to solve the Millennium Puzzle.

Shadi states that when the seven Millennium Items are gathered the door to a better world will open and that the children may travel there, because they have been chosen. The young Aigami thinks that he wants to go to that world and says that he is not afraid of anything because of his friends and family, but Shadi replies that it is his fear.

Bakura's father appears and is excited to see the Millennium Ring, having spent his life searching for it. He offers Shadi a bag of money for the item. Shadi explains that the item is not for sale, but that he can put it on, so he can be tested to see if he is worthy. Bakura's father puts the ring on, but after a few seconds, he is thrown across the room, with the ring detaching from him. Bakura's father is attacked by shadows in the shape of snakes, prompting the young Ryo Bakura to emerge from his hiding place to help him. He runs to his father, who begs him to get the ring. Bakura picks it up and a purple light is emitted.

Yami Bakura is awakened, while the Millennium Ring fuses into Bakura's body, disappearing under his skin. Yami Bakura thanks Shadi for bringing him a nice host and proceeds to attack and fatally wound Shadi. The children run to Shadi, who gives the Quantum Cube to Aigami, just before dying. Yami Bakura continues to attack the children, with Aigami and Sera managing to survive.

In the present, Bakura is shocked by what he has seen. He weeps and claims that it was all the Millennium Ring, but apologizes for taking away someone important to Aigami. Mani arrives with the Millennium Ring, now warped by its evil. He attempts to kill Bakura, before regaining control of himself. He throws Bakura to one side and tells Aigami to run. Bakura is transported to another dimension. Aigami and Mani go to another, where Mani dies and disappears. Aigami considers taking the Millennium Ring, but stops when he hears Yugi calling for Joey.

At Domino City Plaza, Aigami appears before Yugi and admits that he is a Prana, whose real name is Diva. He explains that the "Aigami" Yugi knew was merely an illusion, implanted in his memory.

Inside, the dissolving dimension, Joey falls and his body begins to fade away with the rest of the world. However there is a flash of light and Joey sees Atem. Joey then finds himself back in his own world, where Yugi, Téa and Tristan and relieved to find him, but still worried about Bakura. Aigami then disappears, calling Yugi and his friends interesting. Joey begins to tell Yugi, about him seeing Atem, but stops himself and says it is nothing, before rushing to help find Bakura.

While Aigami is on the roof of a building, he is suddenly abducted and blindfolded by a group of men from KaibaCorp. He is brought before Kaiba, who demands the pieces of the puzzle. After refusing to hand them over, he is taken to Kaiba Land.

During his search for Bakura, Yugi stops at a road crossing just as the lights change. He takes a moment to catch his breath and notices that the traffic is stopped, when it should be moving. Looking into the intersection, he sees that Kaiba is the source of the disruption. Yugi asks him what he is doing there and Kaiba declares that Yugi is to take part in the exhibition Duel at Kaiba Land, no excuses. He shows Yugi the near-reassembled Millennium Puzzle and expresses his belief that Yugi and Aigami have the two missing pieces. Before leaving on his helicopter, he explains that his goal is to face "the other Yugi" and that Yugi alone is of little interest to him.

Yugi sees that the Millennium Puzzle box with his piece is in the road and proceeds to collect it just as traffic begins to move. He almost gets hit by a truck, but is saved by Sera, who teleports him to safety. Yugi thanks her and she says it is up to him to complete the Puzzle or not once again. She also requests that Yugi save her elder brother.

Aigami dreams of himself and Sera, back in Egypt, thirsty and begging people, who regard them as a nuisance. He wakes up tied to a chair in a glass prison, with Mokuba on the other side of the glass. Kaiba monitors their interaction externally. Mokuba taunts Aigami, who affirms that Kaiba will never get both pieces. However, Mokuba claims to already know where the other piece is and shows him pictures of Sera. At the Kaiba Land stadium, which boosts a high attendance, Kaiba Summons "Neo Blue-Eyes Ultimate Dragon" and has it attack Solid Vision fighter jets. He gives a speech to the audience about Dueling and his new Duel Disk. Among those in attendance are Weevil Underwood and Rex Raptor. Yugi and Aigami are introduced and Kaiba announces that he will be Dueling each of them for their pieces of the Millennium Puzzle.

Sera appears before Aigami and apologizes, but maintains that she made the right decision in giving her puzzle piece to Yugi. Aigami is relieved to see that she is okay.

Yugi gets annoyed and demands that he be the one to Duel Aigami. Since Aigami had hurt Yugi's friends and caused Bakura's disappearance, Yugi considers this to be his battle. Kaiba allows it and throws Yugi a new Duel Disk.

Yugi and Aigami begin to Duel. After reducing Yugi to just a few Life Points, Aigami claims he is not doing anything wrong; he just wishes to go the new dimension and leave the current corrupt world behind. He invites Yugi to join him, but Yugi refuses to give up on the current world and its future.

Aigami reflects on his youth, when he was living with an abusive man, who would get children to steal for him. The man would neglect the children and use the stolen money to take care of himself. Shadi appeared before them and immobilized the man. He approached Aigami and pushed against his forehead, causing a gold symbol to momentarily appear. When Sera asked what he did to her brother, Shadi assured her that he was safe. He then proceeded to perform the same action on the other children. Finally, he unfroze the man and used the Quantum Cube to put an end to him.

In the present, Yugi turns the Duel in his favor and defeats Aigami, reiterating that he believes in the future. Aigami disappears after the Duel. While Joey, Téa and Tristan celebrate Yugi's victory, a light appears in the audience, as Bakura is brought back to their world.

Kaiba advances to the field to Duel Yugi for the two pieces. He states that his goal is to bring back "the other Yugi," with whom he has unfinished business. He does not expect the Duel to take long, as he is only Dueling the regular Yugi. Kaiba places the Millennium Puzzle in the center of the field, where it floats in a beam of light. Yugi tries to tell Kaiba that Atem is gone, but he pays no attention and they begin their Duel. A few turns in, Yugi insists that the Duel is pointless and demonstrates by inserting the last two pieces into the Millennium Puzzle. Nothing happens, much to Kaiba's surprise.

Aigami is back in the dimension, where Mani had died, and sees the Millennium Ring again. Sensing his presence, the Ring engulfs him in evil energy. He screams for Sera to save him.

Yugi explains to Kaiba that nothing happened because Atem is no longer inside the Puzzle. Kaiba is furious and accuses Yugi of deceiving him. The two continue to Duel and Yugi eventually attacks Kaiba, who had 2500 Life Points, with "Dark Magician", which had 2500 ATK. Kaiba's Life Points decrease, but he smirks as the counter suddenly stops at 100. The power at the stadium is shut down, prematurely ending the Duel.

People in the audience scream as they suddenly disappear in a wave of shadow. Aigami, now influenced by the evil of the Millennium Ring as Dark Diva, appears and Yugi and Kaiba team up to Duel him.

The Duel is a Shadow Game, where players' bodies fade away as they lose Life Points. Dark Diva reaches a point where he can defeat one of his opponents and chooses Yugi. However, Kaiba redirects the attack to himself and hands Yugi the Millennium Puzzle, before disappearing, demanding that Yugi "call him now". Yugi puts on the puzzle and continues the Duel. Towards the end, Yugi's body reaches its limits and he finds himself incapable of drawing his next card. He apologizes to everyone and begins to black out, but is suddenly engulfed in a beam of golden light. Pharaoh Atem, dressed in the Domino High School uniform, possesses Yugi's body once again. Without speaking, Pharaoh Atem Summons "Palladium Oracle Mahad", who kneels before him. "Mahad" then defeats Diva, whose body reverts to normal, before disappearing. Gold light moves through the stadium, and other people whose bodies had faded away reappear. Yugi and Atem split into separate bodies and stand facing each other. After a moment of silence, Yugi nods and Pharaoh Atem presses on the Millennium Puzzle, making it and himself disappear. Mani is revived and is now with Aigami, Sera, and the other children. Joey, Téa, Tristan and Bakura congratulate Yugi, who informs them that he saw Atem. Joey mentions seeing him earlier too and the group is approached by Kaiba, who is interested in the fact that they saw Pharaoh Atem. Kaiba acknowledges Yugi as a competent Duelist and Yugi thanks him for believing in him. Kaiba gives him a smile and parts ways.

Aigami wakes up in the Plana realm, where Mani informs him that since the Pharaoh had returned their powers were now gone for eternity, but comments that it was for the best.

During the graduation ceremony, Yugi reads his speech, causing Téa to tear up and Joey and Tristan to cry uncontrollably. In Egypt, Aigami and Sera part ways with Mani, on good terms. At the airport, Téa boards a plane and her friends all see her off.

On the KaibaCorp space station, Kaiba is in a pod, on a call with Mokuba, who warns him that what he is attempting is dangerous. Mokuba says that the item in question has not been fully tested and the safety precautions have not been ensured. Kaiba says not to worry and despite Mokuba begging him otherwise, continues with his plan and says that Mokuba is in charge. He activates the Quantum Cube, which is next to him, causing the space station to be covered in gold light, as he shoots down the elevator shaft that connects the station to Earth.

Kaiba appears in a desert, presumably having traveled to the afterlife, and walks to the top of a hill, overlooking a city containing Pharaoh Atem's palace. Kaiba advances to the throne room where Atem is sitting, wearing the Millennium Puzzle. Kaiba activates his Duel Disk. Pharaoh Atem stands up, faces him, and confidently smiles.