Mega Man continues the battle against Dr. Wily's Robot Masters while the clock ticks down. He fights his way to Air Man at the Meteorological Observatory Network high in the sky. Air Man is a little disappointed that Mega Man is not coming at him full strength or is wasting time with words. He nearly defeats the Blue Bomber, but the tables are turned when he is defeated with Rock's Leaf Shield, the last of Mega Man's energy used for ammo. He takes Air Man's weapon and some of his energy while Dr. Light tries to convince him to briefly return to the Lab to be healed. Mega Man declines and once again his eyes turn red as more malicious code is transferred to him via Air Man.
Dr. Light resigns and tells Rock that Agents Krantz and Stern have reported robot attacks at an industrial processing plant and a gem mine connected to it. Mega Man goes there and battles Metal Man. He takes a Metal Blade to the leg and has to dive out of the way of more blades. He uses his Crash Bombs to blow up some gears, giving him enough time to sneak behind Metal Man, copy his power, and plant a Crash Bomb in his back. He survives and throws a series of blades at Mega Man. Rock's metal blades are stronger and cut through Metal Man's attack and the robot himself. Dr. Light declares that Rock has been through enough and tells him that he is going to force him home with an emergency teleport, but Mega Man will not have it. He breaks his helmet's radio and turns off the teleport signal in his chest.
Back at Light Labs, Dr. Light, Roll, and Auto are worrying over Rock. Dr. Light tells Auto to make some phone calls while he tries to remotely hack into Rock's systems and implement an antivirus. Meanwhile, Mega Man conserves energy by avoiding Flash Man's defenses. The Robot Master is confused by his sudden appearance, but recovers quickly and uses his power to take the upper hand. He knocks Rock down, his helmet coming off and avoids the hero's blasts from his Mega Buster. Flash Man appears over him, time frozen, and sees Rock's hair. Realizing he himself is bald, Flash Man wonders out loud why Dr. Wily did not build him with hair. Before he can finish his thought, however, he is attacked and defeated by Quick Man. Quick Man steps on Rock and gives him his helmet and an energy tank. Rock, meanwhile, copies Flash Man's powers.
Revitalized, Mega Man follows Quick Man's bait into a vertical shaft. He uses Flash Man's time stop to avoid a series of lasers and surprises Quick Man when they arrive at the bottom together. Rock and Quick Man begin to battle as Dr. Light's antivirus program is about 70% uploaded. With Flash Man's power, Quick Man can barely lay a hand on Mega Man. He taunts the blue bomber until he stops time and defeats him with a charged blast. He takes a still-smiling Quick Man's powers and jolts as the last of Dr. Wily's virus is uploaded. He is forcefully teleported to Dr. Wily's new castle where the villain himself is waiting. Wily talks to his new robot slave, about how he expected Rock to defeat his Robot Masters just as before and, even in Rock's victory, he would be defeated. He finishes with a laugh that, instead of eight Robot Masters, he has one supreme robot.
Back at Light Labs, Dr. Light is consoling a sobbing Roll, having seen Rock become corrupted. Auto comes in and says that the people he called have come in. The original eight Robot Masters (Time Man and Oil Man included) are standing together and declare that they'll save Mega Man as he did them.