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.
Dr. Wily's new device takes over the city power grid, wreaking havoc for the citizens.
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.
Dr. Wily uncovers a meteor containing power enhancing crystals for robots.
Dr. Wily labors to create a sea fort, stealing ships for parts.
After seeing his new device can hypnotize humans in their sleep, Dr. Wily plots to use it take control of the planet.
Dr. Wily plans to use a robot spider to destroy Dr. Light's computer systems.
Dr. Wily frees a genie, trying to use his magic for world domination.
Dr. Wily unleashes horror movie monster robots, which attack everything in sight.
Dr. Wily's robots discover humanoid lion creatures, which use their strange power to turn people into lions.
Dr. Wily has pulled the moon closer to Earth, creating widespread disasters.
Dr. Light's college for robots leads to the creation of an anti-gravity device. Dr. Wily is out to steal it and reprograms the robot students to help.
Mega Man must prevent Dr. Wily from stealing Dr. Light's new robot, Brain Bot.
Proto Man supposedly switches sides and Dr. Wily plots to replace city officials with robots.
Dr. Wily's amusement park, Fun World, is really a front to hyponotize the visitors.
The evil Vile has arrived from the future, with Mega Man X in hot pursuit.
Dr. Wily uses toys to rob the city blind. But it's all just a diversion so Wily can get his hands on something much more valuable.
Kobayashi spends a long time playing Mega Man 5. When he's fallen asleep Dr. Wily has decided to go out and enter the real world. The next morning Koboyashi activates Mega Man and Rush to enter the real world much to Koboyashi and Akane and their parents' surprise. The father of the family volunteers to take Mega Man to Tokyo where Dr. Wily probably headed to. Mega Man and Rush follow Wily's trail to an amusement park. As Mega Man begins to attack Wily rallys all his robots into a giant war machine called Samurai Man. Mega Man's attacks are futile. Samurai Man tails Mega Man to Kobayashi's school. Kicking a football with a charge attacks Mega Man trashes Wily's robot, but Wily makes his leave. Mega Man has run out of energy and Kobayashi sacrifices his time to skip Judo to help him. He summons Eddy to replenish Mega Man. Rush flies Mega Man and Kobayashi around Japan and suspect Dr. Wily is based in Mt. Fuji. Sure enough Wily is creating a new robot powered by volcanic energy called Magma Man. Mega Man attacks Wily's army of rampaging lava robots. Akane summons Proto Man and Beat to help Mega Man. While Proto Man and Beat take care of the lava robots, Mega Man breaks into Wily's lab and he and Proto Man beat all of Wily's eight Robot Masters. Wily makes his escape in a rocket, but Proto Man diverts his rocket to go back into Kobayashi's video game. After celebrating all Mega Man characters get back into the videogame.
In the New Year's Eve, Akane is calling his brother Yuuta to commemorate, but he is in the last stage of a Mega Man game and gives trouble to go. The two argue and accidentally hit the console. Mega Man gets pulled out into the real world again while Dr. Wily ends up at Dr. Light's lab, where he steals Dr. Light's newest creation, a time machine, and kidnaps Roll. Dr. Light creates a device to follow Wily through the time vortex. While Mega Man rescues Roll, Wily escapes. It is revealed that Wily plans on showering Japan with meteorites on the Tanabata, a day when the citizens traditionally make wishes upon stars. If Dr. Wily wins, he'll make the stars fall on them! Can Mega Man stop Wily in time?
Mega Man is trying to save the day in the game world again when he and Roll get pulled out by Yuuta and Akane to participate in a Japanese festival. Mega and Roll join the kids in the festival with a parade, games and a fireworks display... but one particular explosion transforms into the face of Dr. Wily! Dr. Light repairs the time machine and Mega Man and Roll use it to jump ahead one year in time only to discover that Wily has conquered Japan and raised the entire city of Tokyo high above the surface. Mega and Roll jump back to the past and discover that a typhoon is responsible for this. But, this is not an ordinary typhoon... this is the work of Dr. Wily and his new Typhoon Robot! Can Mega Man and Proto Man save the city from certain doom?
