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 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.
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.
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.
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.
