Fact1: Yugi Muto and closest friends are in final year of High School year after departure of Pharaoh, Fact2: Seto Kaiba has commissioned excavation to retrieve disassembled Millennium Puzzle from ruins of Millennium chamber, Fact3: Diva under alias forges friendship with Yugi and rest of friends, Fact4: Aigami Yugi 's friend Ryo Bakura believes is responsible for death of father-like mentor, Fact5: Jonouchi returns to real word with help of Atem 's spirit
Output: In the opening, KaibaCorp is doing research on the Millennium Puzzle. Suddenly, a mysterious cloaked man is at the underground as one of Kaibas bodyguards tells him that he is behind schedule and to speed up his progress and they will find someone who could. A year after the departure of the Pharaoh, Yugi Muto and his closest friends are in their final year of High School and are talking about what they will do in the future. Meanwhile, Seto Kaiba has commissioned an excavation to retrieve the disassembled Millennium Puzzle from the ruins of the Millennium chamber. The item had previously housed the soul of his rival, Atem, whom he hopes to revive in order to settle their score. The excavation is interrupted by Diva, who faces Kaiba in a game of Duel Monsters and steals two pieces of the recovered Puzzle. He keeps one fragment and gives the other to his sister Sera who passes it on to Yugi Muto, aware that he was the host of the Pharaoh. Diva, under the alias Aigami, forges a friendship with Yugi and the rest of his friends. He takes interest in Yugis friend Ryo Bakura, whom he believes is responsible for the death of his fatherlike mentor, Shadi. Using his Quantum Cube, he transports Bakura and Jonouchi to another dimension. Bakura apologizes and explains that the evil spirit of the Millennium Ring had been responsible. The two are interrupted by Mani, who has become warped by the evil energies of the Millennium Ring. When Yugi, Anzu and Honda find Aigami, Aigami reveal himself as Diva and his plan to eliminate Bakura as well as Yugi. As Diva almost disintegrates the three of them into another dimension, Jonouchi unknowingly returns to the real word, with help of Atems spirit. Kaiba has a computer rebuild the Millennium Puzzle and discovers the last two pieces are missing. He abducts Diva and approaches Yugi, so he can have the two take part in the showcasing of his updated Duel Disk virtual reality technology. He intends to duel, both Diva and Yugi, while gambling their pieces of the puzzle. However, Yugi is furious with Diva over what he did to Bakura and insists he duel him instead, which Kaiba agrees to. Yugi defeats Diva, resulting in Bakuras return to reality, and while dueling Kaiba, Yugi recompletes the Millennium Puzzle to demonstrate that the spirit of Atem is no longer inside it. Origami becomes corrupted by the incredible evil powers of the Millennium Ring, and duels both Yugi and Kaiba. Kaiba sacrifices himself during the Duel and makes a final plea for Yugi to call forth Atem. Yugi succeeds in doing so, and he and Atem defeat Aigami with ease. Atem and the Millennium Puzzle then fade away, and Kaiba returns to reality. The film concludes with Yugi and his best friends, seeing Tea off at the airport as she goes off to pursue her lifelong dream of becoming a professional ballet dancer in New York City. Meanwhile Kaiba uses his technology in conjunction with the Quantum Cube to transport his consciousness to the Netherworld. He approaches Pharaoh Atem, sitting on his throne, who responds with a confident smile.