Kevin Keene and his dog Duke have been transported to Video Land and asked to help defeat Mother Brain.

Mother Brain makes a discovery that Kevin isn't very good at the Bayou Billy video game. So she sets a trap to lure him into Bayouland.

Dr. Wily creates an android that is a replica of Kevin's worst enemy from high school.

Mother Brain challenges the N-Team to an athletic competition on Mount Icarus, thus distracting them from stopping her from finding the Three Sacred Treasures.

The N Team struggle to find weapons with enough power to defeat the magic of the Sacred Treasures.

Kid Icarus feels awful because his height is a problem. Duke discovers a magic lamp and the genie grants Kid Icarus's wish to become bigger.

Dragon Lord and Mother Brain try to turn every dragon evil. The N team rescues Puff, a white last good dragon baby.

Simon gets shot by a "love-at-first-sight" arrow and falls in love with Mother Brain.

After the Computer Mind Mirror of Mother Brain says that Princess Lana is the most beautiful of them all, the Eggplant Wizard makes a poison apple that will make Princess Lana fall asleep.

While the N team tries to get Simon's memory back, Mother Brain gets King Hippo and Eggplant Wizard to brainwash him into thinking he's an N-Team hunter.

Kevin, Lana, Simon, and Duke go to the Mirror World to rescue the princess' father, King Charles. In the mean time their opposites are on a journey to their world.

Mother Brain sets a trap by showing the N team she is defeated and also opens up a warp zone, with Kevin's neighborhood shown on the other side.

On his birthday Mega Man really wishes to become human. So he is ready to pass the Three Challenges to accomplish humanity.