WARNING: Spoilers ahead.
- After Heishin defeats the prince in a Shadow Game, Simon holds him off while the prince shatters the Millennium Puzzle and goes into the future, preventing him from claiming it.
- Kaiba's tournament has Yugi defeating tons of opponents and collecting all 7 Millennium Items to send the prince home.
- High Mage Martis would accept his fate without being a sore loser if he lost to The Prince in a duel for Millennium Item.Martis: "The desert claims me this day..."
- Priest Seto enacts a Xanatos Gambit that spans the whole game. He serves Heishin faithfully at first, seizing control of the palace and Egypt as a whole. When the prince returns from the future, however, he goes behind Heishin's back and gives hints about how to overthrow him. His plan is to gain the Millennium Items that Heishin's Mages guard, use the Items to renew a pact with DarkNite, and rule the world—which he only tells you after you collect the Items, defeat Heishin and do his work for him. If the prince failed in his quest, Seto would defeat Heishin and take over himself. If he succeeded in defeating Heishin, he'd take the Items from the prince instead. The only thing Seto didn't count on was losing his duel with the prince and Heishin having seen his treachery coming and staging his defeat. To top it off, his deck is even stronger than the final boss's, meaning he was prepared for how strong it was.
- The game ending: The Prince saves Egypt from Heishin's regime, Seto's selfish ambition and DarkNite / NiteMare's attempted takeover and becomes the Pharaoh who rules Egypt with wisdom, compassion and trust instead of absolute control and fear like many previous Pharaohs (which means including his late father). The Pharaoh immediately gives order to permanently seal the Forbidden Ruins along with all the Millennium Items instead of keeping those magical artifacts for himself to prevent similar incident from happening again. Very much later, the Pharaoh would be known throughout history as "Yu-Gi-Oh".note
- Given how hard the game is, beating it is an awesome moment for the player, especially the endgame gauntlet which puts you through six or seven difficult fights in a row without the ability to save.
