- The footage from this movie was taken from Yu-Gi-Oh! the Movie, a movie which debuted in Japan on March 6, 1999. The reason the animation looks different in this movie compared to Yu-Gi-Oh! Duel Monsters was because this movie was produced by Toei Animation, the same animation studio that produced the first Yu-Gi-Oh! animated series (erroneously referred to in some communities as "Season Zero"). As with the Toei series, this movie was never officially released in the United States.
- The part where Yugi says that he and Joey live in Japan is a reference to the fact that in the English dub of Yu-Gi-Oh! Duel Monsters, the series was Americanized to where Domino is located somewhere in the United States. "Egyptian Exhibition Expo 2007" pokes fun at this fact as well.
- The reason Kemo's hair looks different in this movie is because he was drawn based on his appearance during the Death-T story arc in the manga. His hair receives its familiar look during the Duelist Kingdom story arc in the manga and Yu-Gi-Oh! Duel Monsters.
- When Yugi asked Kemo if he's supposed to be working for Pegasus, it's a reference to the fact that it's revealed in the manga and a Japanese episode of Yu-Gi-Oh! Duel Monsters that Kemo is actually a spy sent by Industrial Illusions to work for Kaiba Corporation. The English dub of Yu-Gi-Oh! Duel Monsters ignores this fact completely.
- Gary's lines "I musn't run away! I musn't run away! I musn't run away!" are Neon Genesis Evangelion references which were Shinji Ikari's lines.
- Gary Stu is, in fanfiction, the male counterpart of the Mary Sue, since Shougo feels much like a self-insert character for the audience to project themselves into.
- The caption at the end of the credits explaining that Gary was sent to an island to kill off his classmates one by one is a reference to the Japanese movie Battle Royale, where students from a selected class were forced to kill each other on an island due to a law passed by the government to deter the country's youth from rebelling against the adults.
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