The Beginning
E1
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.
Electric Nightmare
E2
Dr. Wily's new device takes over the city power grid, wreaking havoc for the citizens.
Mega-Pinocchio
E3
Mega Man's attempt to become human leads to Dr. Wily working to reprogram him.
The Big Shake
E4
Dr. Wily has found a way to create earthquakes and demands the city surrender or be destroyed.
Robosaur Park
E5
A de-evolution serum that only has an affect on robots is released.
The Mega Man in the Moon
E6
Dr. Wily plots to gain control of a giant laser on the moon. Mega Man follows him up into space to stop him.
20,000 Leaks Under The Sea
E7
An underwater mining operation falls under attack by Dr. Wily, who traps Dr. Light and Mega Man in a small prison.
Incredible Shrinking Mega Man
E8
Dr. Wily intends to use his new shrink ray on several cities, but his Robot Masters turn it on Mega Man.
Bot Transfer
E9
Dr. Wily has built a teleporter, which doubles as a body switcher, resulting in Mega Man and Snake Man trading bodies.
Ice Age
E10
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.
Cold Steel
E11
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.
Future Shock
E12
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.
The Strange Island of Dr. Wily
E13
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.