Mega Man, Rush and Roll are defeated by Dr. Wily and his robots at the city airport. While he makes repairs, Dr. Light recalls when he created Mega Man.

Mega Man's attempt to become human leads to Dr. Wily working to reprogram him.

Dr. Wily has found a way to create earthquakes and demands the city surrender or be destroyed.

A de-evolution serum that only has an affect on robots is released.

Dr. Wily plots to gain control of a giant laser on the moon. Mega Man follows him up into space to stop him.

An underwater mining operation falls under attack by Dr. Wily, who traps Dr. Light and Mega Man in a small prison.

Dr. Wily intends to use his new shrink ray on several cities, but his Robot Masters turn it on Mega Man.

Dr. Wily has built a teleporter, which doubles as a body switcher, resulting in Mega Man and Snake Man trading bodies.

Dr. Wily gets his hands on some super freeze technology, which he hopes will force city leaders to leave. But Ice Man gets the feeling Air Man is replacing him and switches sides.

Dr. Wily's robots disguise themselves like a rock band to unleash a mind controlling music. Only Mega Man, Roll and a young deaf girl remain unaffected.

Dr. Light's time machine sends Mega Man to a future where Dr. Wily controls the planet. Mega Man must find a way home and save this future.

Dr. Wily's new invention strands the good guys and the bad guys together on an island. They'll have to work together to escape the island.