At the KaibaCorp space station, Seto Kaiba observes a virtual reconstruction of the Millennium Puzzle.
In the Valley of the Kings, the Shrine of the Underworld is excavated by KaibaCorp, with Mani, among the workers. One of the other works 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 struggles to remember what it is he has to tell Yugi. Yugi gets impatient and he finally remembers it by telling Yugi that Tea Gardner is going to be late, so Yugi must wait for her at their meeting point.
At the rendezvous point, Tea greets Yugi with a shoulder bump and asks if he has been waiting long, to which Yugi replies that he has not.
Meanwhile Joey Wheeler hurriedly cycles to school. His carelessness causes him to get soaked by a man emptying a bucket of water and nearly knock over a policeman. Yugi and Tea 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 closes it.
At lunchtime on the roof of the school, Yugi and his friends discuss their futures. Tea wishes to study dancing in New York. Tristan is unhappy with the job, he has lined up working for his father. Joey would like to become a professional Duelist, but needs to retrieve his Duel Disk, which has gotten old and broken. Yugi reckons he will stay working in Kame Game, helping his grandfather, because he wishes to become a game designer himself and create a game that will be enjoyed by children, all over the world. Tristan and Joey support his idea and offer to help him out. While Tea says that she is certain Yugi will succeed.
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 Tea. He and Joey have received back their Deck and Duel Disk respectively, that their teacher confiscated. 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 Kudaragi and his gang, with Kudaragi commenting on Aigami's cute face and making provocative remarks. Joey jumps down from the bridge and approaches the group. Aware of Joey's past in a gang, Kudaragi and his companions let the matter drop for the time being and leave Aigami alone for the time being, but Kudaragi instructs Aigami to meet him at the KaibaCorp construction site later and threatens him, should he not show up. Aigami thanks Joey. While he tells Tea and Yugi that he is fine, before leaving.
Later at the construction site, Kudaragi 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. Kudaragi and his gang are disintegrated and drop their camera. Aigami starts to walk away, but returns to collect the camera.
At a church-like setting, Atem dressed as he was, while sharing Yugi's body and has two additional gold armbands. He walks through a set of doors, where he faces 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 Kaiba a bottle of water and comments on how good the system, but Kaiba is not happy. He deems the Duel imperfect, because he had not accurately recreated Atem, based on his memories. 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, Tea, Tristan and Bakura are sitting at Devlin's cafe, being served by Duke Devlin, while in the news, it is reported that Kudaragi and his gang have disappeared. Nearby, Joey is wearing a dog costume, walking around, handing out balloons. Bakura mentions how recently he has been getting the feeling he is being watched, which Tea points out is due to the girls that were obsessing over him, who are currently stalking him.
Aigami teleports to the mall, where he stands on a higher level and watches over Yugi and his friends. He reflects on a time he was on 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, causing him and Joey to start fighting. Tea tries to break them up, but Joey eats her ice cream, while continuing to fight. Joey's boss, Mr. Clown, sees this and fires Joey, who begs him not to.
In the Valley of the Kings, 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 questions how he knew his name and Kaiba asks how 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, group 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.
They Duel using a dimensioning ruleset. Kaiba is outperformed at first, but resolves that he cannot lose, since he must face "Yugi", before correcting himself and saying "Atem". Having used virtual cards up until this point, Kaiba slams his hand into the ground and pulls out a physical card, "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", raising its ATK to infinity, and then attacked and defeated Aigami.
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.
Meanwhile Joey wakes up 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 (凡骨 bonkotsu) like him will never be able to afford it and teasingly asks if he wants it. Joey falls off the blimp, but wakes from his dream, during the graduation rehearsal at school, 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, he managed to swipe from the Millennium Puzzle, 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 Burger World. The group tell Aigami stories about their adventures together, including their trip to Egypt, which Aigami says he would look to hear more about. Joey shows his Deck to Aigami, 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 is thinking to himself "Wait for me... Yugi".
Aigami, Bakura and Joey are on their way to visit Yugi, who has arranged to face Aigami in a friendly Duel. Aigami shows Joey and Bakura his Quantum Cube, which he says is a Deck case, which was given to him by someone 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 the Kame Game shop, 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 plateau 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 about it. While being unsure why he is sharing this information. Aigami uses his powers on Bakura, who cries out that he does not want to remember. Joey tries to intervene, but a group of children appear and tell him that Aigami wishes to speak with Bakura and he is being a bother. Joey is sent to another dimension, where he finds himself in a street, with other people walking past him. The world begins to dissolve around him and Aigami appears in the sky, taunting him, saying that he is worthless and cannot escape.
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 see Joey's abandoned bike and they meet with Tea.
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, where Shadi, 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 that is his very 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 landlord 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 one 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, Tea 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, and not to make 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 fragments 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 for 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 on 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, Tea 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," whom he has unfinished business with. 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. Without touching it, he becomes engulfed in its evil and 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 darkness. Aigami, now influenced by the evil within the Millennium Ring, which is now fused into his chest, 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. Aigami manages to defeat Kaiba, who hands Yugi the Millennium Puzzle, before disappearing and demands Yugi to "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. Atem, dressed in the Domino High School uniform, appears superimposed over Yugi and the two draw together. Yugi and Atem Summon "Mahad the Protector Priest", who kneels before them. Using "Mahad", the two defeat Aigami, whose body reverts to normal, before disappearing.
However a gold light moves throughout 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 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, Tea, 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 Atem. Kaiba acknowledges Yugi as a competent Duelist and Yugi thanks him for believing in him. Kaiba gives him a smile and parts ways.
During the graduation ceremony, Yugi reads his speech, causing Tea to tear up including Joey and Tristan to cry uncontrollably. In Egypt, Aigami and Sera part ways from Mani, on good terms. At the airport, Tea leaves for America and all 4 of her friends see her off.
On the KaibaCorp space station, Kaiba is on a call with Mokuba, who is warning him of something 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, he gets into a pod, with the Quantum Cube next to him. He also leaves KaibaCorp to Mokuba. He activates the cube, 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 and walks to the top of a hill, overlooking a city containing Atem's palace. Kaiba advances to the throne room, where Atem is sitting, wearing the Millennium Puzzle. Atem stands up, faces Kaiba and smirks.
- Shunsuke Kazama as Yugi Muto & Virtual Yami Yugi aka Atem
- Kenjiro Tsuda as Seto Kaiba
- Hiroki Takahashi as Joey Wheeler
- Maki Saito as Tea Gardner
- Hidehiro Kikuchi as Tristan Taylor
- Rica Matsumoto as Ryo Bakura & Yami Bakura
- Junko Takeuchi as Mokuba Kaiba
- Ryo Naito as Duke Devlin
- Tadashi Miyazawaw as Solomon Muto
- Nozomu Sasaki as Shadi
- Kazuhiro Yamaji as Bakura's Father
- Kazunari Kojima as Black Magician
- Yuki Nakao as Black Magician Girl
- Measami Iwasaki as Roland
- Shoma Takeda as Young Deeva
- Rina Endo as Young Sera
- Takeru Takeyama as Young Mani
- Kendo Kobayashi as Kudaragi
- Kento Hayashi as Deeva
- Kana Hanazawa as Sera
- Satoshi Hino as Mani
- Dan Green as Yugi Muto & Virtual Yami Yugi
- Eric Stuart as Seto Kaiba
- Wayne Grayson as Joey Wheeler, Solomon Muto, Shadi & Roland
- Amy Birnaun as Tea Gardner
- Greg Abby as Tristan Taylor
- Ted Lewis as Ryo Bakura
- Tara Sands as Mokuba Kaiba
- Marc Thompson as Duke Devlin & Bakura's Father
- Michael Crouch as Young Bakura & Yami Bakura
- Daniel J. Edwards as Black Magician
- Bella Hudson as Black Magician Girl
- Billy Bob Thompson as Kudaragi
- Daniel J. Edwards as Deeva (Young & Older)
- Laurie Hymes as Sera (Young & Older)
- Tamir Cousins as Mani (Young & Older)
- In celebration of the film and franchise in general, TV Tokyo began airing a remastered digital edition of the 2000–2004 Yu-Gi-Oh! Duel Monsters anime in Japan.
- This will be the third theatrical release of a Yu-Gi-Oh! film after Yu-Gi-Oh! The Movie: Pyramid of Light and Yu-Gi-Oh!: Bonds Beyond Time.
- Creator Kazuki Takahashi published a new one-shot called "TRANSCEND GAME" in Weekly Shonen Jump. The two-part story is set after the events of the Yu-Gi-Oh! manga and the beginning of The Dark Side of Dimensions. Part 1 was released in the 19th issue on April 11, 2016. While Part 2 was released in 20th issue on April 18, 2016.
- The film's teaser trailer was first shown in a panel featuring Kazuki Takahashi at San Diego Comic-Con 2015. It was later uploaded to the official yugioh.com YouTube channel. The trailer credits Kazuki Takahashi for the story, script, character design and as executive producer.
- The film is to be release in 2016, the 20th anniversary of Yu-Gi-Oh's debut (it first appeared as a manga in September 1996).
- The first time in the English version of the movie, where every thing shown in Japanese writing such as articles, shops and etc that won't be translated into English.
- Even though the film is uncut entirely. A goof in the English version is that during duel with Kaiba, Virtual Yami Yugi calls Black Magician "Dark Magician" and even calls Black Magician Girl "Dark Magician Girl". Not only that Yugi himself says the same thing during his duel against Kaiba.
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