The city airport is running smoothly; robot workers are doing their jobs as usual. Suddenly, Dr. Wily and of his robots : Elec Man, Bomb Man, Fire Man, Guts Man, and Cut Man crash the scene. Dr. Wily, along with Proto Man, watch from above. "They call me crazy...insane...mad! ...Well I'm showing them!" - a quote from our favorite evil scientist himself. Airport staff calls in Mega Man for help. Dr. Light mentions that he and Wily used to work together. Roll, Mega Man's sister, tries to leave with Rush and him, but Mega Man stops her. Eddie hands Mega Man an energy boost. Mega Man and Rush then jet for the airport.
Mega Man doesn't receive the most pleasant greeting, as Wily shouts, "Attention all robots! Destroy Mega Man!" Yikes. Mega Man dispatches of Bomb Man quickly, then we listen to Proto Man and Wily bicker a bit. Proto says "I'll obey you...when I want to". Proto and Mega Man have a quick duel. Meanwhile, Roll is in trouble, Guts Man nearly squashes her, until Mega Man gets her out of the way, but absorbs all of the impact. Wily, thinking he has destroyed Mega Man, leaves the scene.
Back at the lab, Dr. Light is unsure of whether he can restore Mega Man fully. Roll, Rush, and Eddie look on uneasily. Dr. Light starts reminiscing, and we go on a flashback for a while...
"Dr. Wily was my assistant..." says Light. He and Wily, shown working together, are in the lab. Light shows Wily his first prototype robot, and turns him "on". The robot goes berserk and starts wrecking things. Light decides that the computer guidance system within the robot is to blame for the robot's destructiveness, and says they will have to start over. Dr. Wily, having designed that guidance system, claims that it cannot be to blame. Light says “No, I’m sure it’s the… GUIDANCE SYSTEM” and leaves the room dejected. Wily quickly becomes bitter, believing Light is wrong and is holding him down. He starts to make off with the prototype plans, when Dr. Light walks in and sees him. Light chases Wily, but he gets away.
We go to Wily's own lab , Wily talks to himself, calling Dr. Light jealous, and says that "no one knows my genius". He builds Proto Man, and begins dreaming of world domination with the help of his future robots.
Meanwhile, back in Dr. Light's lab, he is about to turn his new robot, Rock (Mega Man) on. Rock appears friendly, and Light tells him that he was programmed to be humanlike, which pleases Rock. Light then introduces Rock to his sister, Roll, a household robot. He then shows Rock and Roll his other new creations: Cut Man, Guts Man, Ice Man. Suddenly, Proto breaks in the lab with Dr. Wily, and Wily puts those three robots under his control by reprogramming them. They will now always obey him Wily, with the help of his new followers, manages to take Rock and Roll, who are pretty much helpless, back to his Skull Castle.
Dr. Wily wants to reprogram Rock and Roll, while acting like a maniac. Proto tries to convince Rock to come to the other side, but Rock's good conscience will not sway. He tells Dr. Wily that Dr. Light has an army of super robots headed their way. Wily, knowing that robots cannot tell lies, believes him, and unties him to let Rock show him what to do. Rock and Roll manage to escape, Wily is furious, and wonders how Rock lied to him. Back at Light's lab, Rock asks him how he was able to lie. Light explains that it was the human emotion that allowed him to make the choice. Realizing that Wily and company will be back soon, Dr. Light decides to turn Rock into a powerful warrior robot, and calls him Mega Man. Once revived, Mega Man is shown Rush, his robotic dog companion and transportation. Roll has also been improved a little bit for combat, though Mega Man feels she should stay out of the fighting.
Mega Man wakes up and remembers what is going on. He decides to let Roll come along with him and Rush. Eddie gives him double energy power this time. Wily is still at the airport, again with his robots. Mega Man and company crash the scene and begin to battle with Wily's robots. He steals Cut Man's power and fires a cutblade at him; Cut Man flees to Wily's flying contraption Mega Man gets Ice Man's power, while Roll and Rush take care of Fire Man. Proto Man and Mega Man duel once again, but Wily escapes with Proto Man and leaves the scene. Mega Man, at least for the time being, has stopped Dr. Wily and saved the day. But we all know he'll be back...
