After the events of the first story, the government decides to dispose the six robots of Dr. Light due to the fact they were considered dangerous, despite being under Dr. Wily's control. Rock runs to the disposal building they are located in, despite the large storm, and is attacked by one of the robots covered in the robes. He then reveals himself, and tries to attack Rock, who changes into Mega Man, but fails due to the Air Shooter. He is about to be finished off, but Flash Man appears, and he joins in the brawl. Meanwhile Wood Man is sent to the disposal plant to find the six Robot Masters, and reactivates them. He offers them their lives back by joining him, or else they would be destroyed. They choose not to do join them, despite their fate, but Elec Man and Ice Man decide to (but Bomb Man discovers they were trying to trick Wood Man),and they go with him. After Air Man's robots and Flash Man are defeated, the storm passes, but Metal Man, and Crash Man appear to aid Air Man, and Wily makes a broadcast. He states throughout the city he built several "Skull Satellites", that would go into space and destroy the earth if he didn't achieve world domination. Mega Man is then aided by the other four of Dr. Light's Robot Masters, and Roll passes him Item-2 to get to the base, Crash Man tries to shoot him down, but instead passes his Crash Bombers to Heat Man to chase him.