The students of Duel Academy went on a field trip to Domino City. Among them was a tarot card reader, Sartorius, who wished to defeat Yugi Muto and the other legendary duelists. Strange circumstances led Jaden Yuki to meet Yugi Muto and Joey Wheeler. Sartorius contacted KaibaCorp to plot his scheme.
The idea of the film came from Kazuki Takahashi's unmet expectations from seeing Mazinger Z Vs. Devilman in his childhood. He came up with the idea about a year after Yu-Gi-Oh! GX had begun broadcasting.
Takahashi contemplated reviving Atem, but didn't want to betray the theme of the original story.
After the idea was dropped, Takahashi commented that it was fun to see Yugi and the others in his head after such a long time and that Yugi facing Jaden couldn't happen as it would be a hero facing his comrade.
Ideas from the film were used in season 2 of Yu-Gi-Oh! GX when Jaden and his friends do take a field trip to Domino City and Sartorius was retooled to be the villain of that season, rather than of the movie.
Despite Takahashi's comments, the last two episodes of Yu-Gi-Oh! GX featured Yugi dueling Jaden albeit in a different context. The two also meet in Yu-Gi-Oh! 3D Bonds Beyond Time, along with Yusei Fudo. Yu-Gi-Oh! The Dark Side of Dimensions also brings Atem back to help Yugi out.