After getting knocked out in battle, Mega Man has a dream flashing back to when he was first created by Doctor Light and how he reprogrammed him into the Blue Bomber he is today.
Dr. Wily takes over the power grid with a device that allows him to control machines through electricity. He then proceeds to attempt to take over the city with soda machines and monorail cars and only Mega Man can stop his plans.
Dr. Wily tricks Mega Man into thinking he will get changed into a real human boy when he's actually putting a mind-controlling chip into his helmet.
When Dr. Wily creates a new machine made to create earthquakes, Mega Man must try to find it and destroy it.
A devolution acid that effects robots is raining in Robosaro Park, Dr. Wily's robots aren't effected by it because he had them vaccinated and Dr. Light must find an antidote to stop it from happening.
Mega Man follows Dr. Wily to the moon where he and his robots are building a new laser machine.
Dr. Wily attacks an underwater mining operation, then tries to get rid of Dr. Light and Mega Man with a fake laboratory that turns out to be a mobile prison.
Dr. Wily creates a machine that he uses to shrink big cities and sell them to millionaires. He also shrinks Mega Man and Rush in the process.
Mega Man switches bodies with Snake Man and has to try to survive in his new body without causing any trouble.
Dr. Wily steals a super freeze technology to create a giant glacier and freeze cities, drive out their leaders, and replace them with his robots. Ice Man, however, decides he's being replaced by Air Man and double-crosses Dr. Wily.
A new hit song by the band, Cold Steel, is causing people all over the world to get hypnotized. Little do they know, the band is Wily's robots in disguise.
Mega Man is accidentally booted to the future by a time machine, where he discovers that the evil scientist Dr. Wily has taken over the planet. Mega Man must find his way back to his own time so that he can reverse this horrible future.
A new invention of Dr. Wily's goes haywire on an island. He and his robots reluctantly join forces with the good guys to try to reverse it.
Dr. Wily finds a meteor with crystals that can super-power his robots. However, the crystals also have a nasty side effect of overloading the circuits of the robots using them after a random period of time.
After several ships go missing, Megaman along with Roll and Dr. Light search the seas and find Dr. Wily plundering the world's shipping fleet.
After seeing his new device can transfer his robots into his dreams and then hypnotize humans in their sleep, Dr. Wily plots to use it to take control of the planet.
Dr. Light creates a supercomputer that can defend military bases. Dr. Wily wants to destroy the supercomputer and take over the military bases. He uses a robot spider to drain the city of all its energy, to destroy the supercomputer.
An archaeological trip leads Megaman to face Dr. Wily and an ancient evil spirit locked in a gold chest.
Dr. Wily tries to film a movie with robots he made based on the classic Universal movie monsters, but Mega Man interferes with his plans.
Dr. Wily's robots discover humanoid lion creatures who use their strange powers to turn people into lions and make robots obey them. Both Dr. Light and Dr. Wily are transformed and it's up to Mega Man to change them back.
Dr. Wily invents a device to bring the moon closer to the Earth, and Mega Man has to stop him before he causes chaos all over the world.
Light creates a college to school robots to teach them of his newest invention: an anti-gravity device. Dr. Wily on the other hand decides he wants the device for himself and attacks the school, reprogramming many of the students.
Mega Man must prevent Dr. Wily from stealing Dr. Light's new robot, Brain Bot. He is too late and Dr. Wily gets his hands on him, but thanks to Mega Man he doesn't have time to make any adjustments and the robot ends up helping Mega Man.
Proto Man seemingly switches sides when Dr. Wily plots to replace city officials with robots. Mega Man is wary of Proto Man's true motives. He then overhears Proto Man talking to Dr. Wily about his plot and stops the whole thing.
Dr. Wily runs an amusement park that hypnotizes guests into being robots.
The evil Mavericks Vile and Spark Mandrill have arrived from the future and the two of them quickly prove far too powerful even for Mega Man. He is saved by Mega Man X who's in hot pursuit of the two Mavericks.
Dr. Wily reprograms a bunch of dolls and other toys to perform robberies all over the city. However, it's all just a diversion so Wily can get his hands on something much more valuable: a giant black pearl. Mega Man has to stop Dr. Wily.
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?
