A huge celebration at the World Robot Expo is shattered by the sight of a flying saucer streaking across the sky. But instead of holding little green men, this saucer holds one very mad scientist! Armed with a mind control machine that transmits a sinister signal. Dr. Wily is ready to mesmerize all the robots of the city into an army of mindless metallic mercenaries!

Battling the effects of Wily's mind control machine, Mega Man and his robotic reenforcements, Rush and Beat must blast to molten metal an army of foes led by eight of Wily's greatest robot masters! And should Mega Man survive, Dr. Wily is waiting to unleash the heavy artillery with his latest creation, the awesome Wily Tank!

In the year 20XX, a few months after Mega Man III, scientists all over the world have gathered in the annual World Robot Expo, where they show their latest creations, robots developed for world peace. Dr. Light took part in the expo alongside Rock, Rush, and Beat. A variety of industrial robots were presented, but suddenly a dubious UFO appeared in the sky. Dr. Wily reveals himself and announces that he will be using the robots from the exposition to help him in his quest for world domination, using a radio wave to control the robots. Rock and Rush aren't affected due to their circuits having a strong sense of justice, but Beat loses four of his parts in the commotion. Dr. Light quickly returns to his laboratory to change Rock into the combat robot Mega Man. Meanwhile, Dr. Wily scatters the controlled robots to cause havoc in the city. Ready for battle, Mega Man must stand up against the expo's newly developed, high-performance robots and stop Dr. Wily, and if possible also find the parts Beat dropped so he can assist him.