Five thousand years ago, an unnamed heroic Pharaoh imprisoned List of Yu-Gi-Oh! characters#Anubis, the Egyptian lord of the dead, after he tried to destroy the world by persuading the kings to play the mysterious Shadow Games. In the present day, Anubis' tomb is uncovered by archaeologists, amazed with his strongest and most valuable treasure: the Pyramid of Light. A devastating spiritual force unleashes from the relic and liberates the Egyptian sorcerer. Anubis, now free, intends to conclude his plan.
未来から来た謎の敵「パラドックス」によって、不動遊星の「スターダスト・ドラゴン」が奪われてしまった。不動遊星はパラドックスを追ってタイムスリップし、精霊と通じる遊城十代と伝説のデュエリスト・武藤遊戯に出会い、3人はパラドックスとの壮絶なデュエルを繰り広げる。
In the opening, KaibaCorp is doing research on the Millennium Puzzle. Suddenly, a mysterious cloaked man is seen at the underground shrine as one of Kaiba's bodyguards tells him that he is behind schedule and to speed up his progress, and that they will find someone who could if he cannot. A year after the departure of the Pharaoh, Yugi Muto and his closest friends are in their third and final year of Domino High School and are talking about what they will do in the future.