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.
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.
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.