Beating Rebecca, Panik, and the Millennium Guardian at the start of the game, given how poor your starting deck is.
Minor manga character Hanasaki dresses up as the superhero Zompire to kick out one of the Neo Ghouls, and wins.
When dueling Arkana, your character gets the option of an awesome line.
Arkana: I'll give you two choices. Do nothing but watch this stunning show as I defeat this woman... Or step in and be magically defeated by me! Player: I'll let you surrender.
If you pick the other option, Arkana gets an awesome comeback.
Player: I'm going to win! Arkana: Are you that anxious to be humiliated?! I will have you begging on your knees before it's over!
When the Neo Ghouls take over the Egypt Exhibition, you have to battle your way through 5 opponents without being able to heal in between. Clearing this challenge makes Yugi and Joey declare that you are an awesome duelist.
Seto Kaiba takes out 10 Neo Ghouls by himself, one after the other.
Bandit Keith is at his best in this game. He usurped the Ghouls from Marik, the main villain of Battle City who controlled him in the anime. Then he holds Ishizu hostage to force you to hand over the Millennium Items. When you then defeat him in a duel, he ups the ante and orders you to hand over your Egyptian God Cards. Both times, you have no choice but to do as he says.
Due to looping sprite animations, Para and Dox can backflip up flights of stairs.
Yami Yugi, after being out of commission for nearly the entire game, unleashes the full power of Ra on Bandit Keith, frying him with a lightning bolt.
Reshef possesses Bandit Keith and makes him break the Millennium Puzzle, allowing Para and Dox to steal it—and Mokuba.
Defeating That One Boss, Marik, to unlock the true power of the Winged Dragon of Ra.
On the way to Pegasus's castle, Joey has an introspective moment as he wonders why Pegasus is doing all this and calls him out on it.
Joey: I don't know much about savin' the world, but I wanna know why Pegasus lost his pride as a true duelist. Pegasus was always a master duelist. No one would argue with that, especially since we faced him firsthand. So why would he resort to even dirtier tricks than before? I'm not the smartest guy on the planet... But I know that Pegasus isn't a real duelist anymore!
Yugi and Joey's You Shall Not Pass moments near the end of the game. Joey takes on Panik and the Mimic of Doom at the same time by himself, and Yugi does the same with Para and Dox. For added awesome, this is regular Yugi, not Yami.
Joey, Yami Yugi, and Kaiba weakening Reshef with their signature monsters to the point where he's beatable.