When two strange meteors fall to Earth, Megaman heads off to the strange island that serves as the crash site. Once there, he sees his arch-enemy Dr. Wily stealing one of the meteors! Megaman looks into a huge crater and sees that the "meteor" was a robot. After shipping it off to Dr. Light, Megaman departs to defeat four of Wily's Robot Masters- Clown Man, Tengu Man, Frost Man, and Grenade Man. Upon each of their destructions, a mysterious purple orb with a skull-shape inside comes out. When Megaman asks about these, the robot that fell to Earth activates, and introduces itself as Duo. The purple orbs are "evil energy", which has the potential to destroy planet Earth! Duo leaves to destroy the evil energy already affecting the Earth, while Megaman is left to destroy the other four Robot Masters that have an orb of the stuff-Search Man, Astro Man, Sword Man, and Aqua Man. Can Megaman defeat Wily and stop the evil energy?