Though elements of the Dawn of the Duel story arc from season 5 of the show are used, the plot of this film greatly mirrors that of season 4. An ancient enemy arises and uses the Pharaoh's power against him in some way, they wear powerful stone and use its card counterpart to surround the field and prevent any interference, Yugi is prevented from using the God Cards until the end, after the enemy loses the final duel from a combined attack of 3 Legendary Monsters they take the form of or combine with a great beast to attack Yugi and his friends (Joey even uses some of the same monsters to fight both), the enemy uses Pegasus to manipulate Kaiba when he seeks him out for answers, Pegasus later shows up to provide background information and other answers for Yugi and/or his friends, and Yugi and the Pharaoh are separated for a sizable portion of the story and are only reunited once the enemy suffers some form of defeat and loses what was originally going to be the source of power for their attack on the world.
Four different Yu-Gi-Oh! cards were given away at theaters in the USA. They were of: Pyramid of Light, Blue-Eyes Shining Dragon, Sorcerer of Dark Magic, and Watapon.
The original Japanese story calls for the Pharaoh's past to take place "3000 years ago", but the English translators misread this as "3000 BC". The English version thus puts the story 5000 years ago, but some believe this was intentional: nothing is known about Ancient Egypt 5000 years ago, and therefore the non-existence of Pharaoh Atem cannot be proven (or disproved).
An image of "Blue-Eyes Toon Dragon" appears on the label of Pegasus's red wine bottle.
The movie was written originally for an American audience, although it was made in Japan.