Blizzard Buffalo and Chill Penguin can be seen frozen in the background of Frost Walrus' stage.
First game to feature Zero as a fully-playable, non-restricted character.
After beating 4 mavericks, X has to visit a mini-stage to fight Colonel. Zero doesn't have to do this, instead a cut scene of a duel between the two is shown.
Double only appears in X's story, while Iris only appears in Zero's story.
In Jet Stingray's stage, he attacks you BEFORE you reach his boss room, a rarity for any game in any Mega Man series.