Depending on which Robot Master you defeat last, the following cutscene showing the memory of Spoiler:Dr. Wily convincing them to join him will be shown from different points of view, with the last Robot Master defeated being removed from the shot.
Using the Laser Trident will give Mega Man the same color scheme as his appearance on the original North American box art for Mega Man.
A device used in Dr. Light's Laboratory to hold certain items during cutscenes appears to be the same device used in the opening cutscene of Mega Man 4 that turns Rock into Mega Man.
For some reason, the word 'Sigma' is censored if you enter it at the player naming screen.
According to Capcom, there is a secret that no one has found in Mega Man 9. To this day, no one has any idea what the secret is, or if Capcom is telling the truth about it.
Bass, Mega Man's rival from Mega Man & Bass, makes a cameo appearance on Dr. Wily's monitor in the ending cutscene.
According to the booklet of the Rockman 9 Arrange Album, Bass, known as Forte in Japan, was absent from the game because he was undergoing "adjustments" during the events of Mega Man 9.
Both Splash Woman and Hornet Man had their genders swapped; they were each originally designed as Ocean Man and Honey Woman respectively. The reason they were changed was because Keiji Inafune wanted the female robot master to be represented by a mermaid.
Chun Li from the Street Fighter series makes a cameo appearance as a newscaster in the introductory cutscene.