It is the year 20XX. Since Dr. Wily's last defeat, the Blue Bomber has seen peace return.

Just when people forgot all about Dr. Wily, robots all over the world began going crazy. It soon became apparent that these robots were those created by Dr. Light. As phone calls came pouring into Light's lab, Dr. Wily interrupted all television programs to announce that these robotic riots were not his doing. He then continued to show video evidence that proved Dr. Light's involvement in the recent violent outbreaks. To make matters worse, Wily gave the account number to his personal bank account and announced that he would accept donations to build his own robot army to counter that of Light's. Mega Man quickly volunteered to clear Light's name and was sent out to investigate the source of the problem.

Before long, the police came to Light Labs to arrest the good doctor, but Light went along quietly to prove his innocence. Meanwhile, Mega Man went after the Robot Masters and, after he defeated a few of them, discovered that they were scheduled to be decommissioned and sent to the junkyard because they had reached the expiration date assigned to them by the government. Once the final Robot Master had been taken down, Mega Man brought back one of the robot's internal memory units to Auto for investigation. As it turned out, Dr. Wily had reprogrammed the robots, who were scheduled for demolition, to rise up against their human masters rather than be destroyed. All the robots wanted to do was have a purpose, and they certainly did not want to be sent to the scrap heap.

After they had viewed the video, Dr. Wily burst into their lab and stole the memory circuit and then withdrew to his newly constructed Wily Castle. Mega Man made his way through the fortress, fighting powerful robots built with the money Wily received from donations from those concerned with the robot uprisings. In the end, Mega Man defeated Wily once again, and showed him footage of every single defeat he had dealt Wily. Although Wily seemed contrite and apologetic, he tricked Mega Man into thinking that Dr. Light was, in fact, imprisoned in a jail cell in the next room. Although Proto Man warned him that it was a trap, Mega Man went to investigate the cell and was electrocuted by the Dr. Light decoy that was in the cell instead. As Wily's lab self-destructed, Proto Man returned and teleported Mega Man out of the lab just in time.

In the end, Light was released from prison. He then found useful purposes for all of the Robot Masters he had designed, which had reached their expiration dates.

Although the ending states that Dr. Wily was nowhere to be found after the destruction of his base, the credits show Concrete Man chasing him.