Dr. Wily is cleaning Mega Man's armor (Whom, now equipped with a purple scarf, resembles Mega Man?) when his alarms go off. He turns to find the disturbance and sees that the eight original Robot Masters are ambushing his castle. Working as a team, the group defeats his first line of defenses and enter the castle. They are confronted by Wily's Mecha Dragon and he sends in the corrupted Mega Man for good measure. Elec Man is damaged by the dragon but the Robot Masters manage to subdue the Blue Bomber. They use a packet to download the remaining 2% of Dr. Light's antivirus program into Mega Man, restoring his free will. He leads the charge, defeating the Mecha Dragon.
Elec Man is helped out of the building by Fire Man, Ice Man, and Cut Man. Rock is also given a set of items to use to help him throughout the castle. Using a pair of Item-2 fliers, the remaining Robot Masters continue. Time Man, Oil Man, and Guts Man are on one board when they are attacked by the Guts Tank. The three take it down while Mega Man and Bomb Man go on. Finding themselves in a maze, Rock uses Crash Bombs and Bomb Man uses his own attack to destroy the walls. Out of ammo, Bomb Man stays behind.
Rock enters the final room where Wily is waiting in an attack ship. Rock wants to use all his new weapons but the first, the Metal Blades, destroys the ship in just one set of three blades. He comments on how cool the blades are and opens the ship's casing to face Dr. Wily. Wily begins to transform and tells Rock that he cannot stand up against alien technology. He becomes an alien and begins to attack Rock as the room around them becomes space. Mega Man quickly discovers the room is a hologram and attacks the projector on the roof. The alien and the fake space disappears, revealing Wily operating machinery. Rock pulls Wily down but the evil man both activates the self-destruct and escapes through a trap door.
Rock quickly flees the building, gathering all the Robot Masters as he passes by them. They manage to escape just in time. Later, the group has a party at Light Labs. Elec Man is almost done being repaired when Dr. Light reveals he has built a new support unit. When Rock asks what he means, Light whistles and Rush comes charging in, leaping into Rock's arms and licking him affectionately. Auto wonders if he should pack up and head back to his shop, but Light tells him to stay, that Dr. Wily will raise his head again soon. Wily, somewhere else, is setting his sights on the Lanfront Ruins.