Dr. Light and Dr. Wily were brilliant scientists in the field of robotics, who worked together in a laboratory trying to advance the science. One day, they finished an extremely advanced prototype, but shortly after being activated, it started destroying the laboratory. Dr. Light immediately believed that the prototype's guidance system, which Dr. Wily had personally programmed, was the source of the problem and concluded they would start over again. Angered, Dr. Wily attempted to steal the plans later that night, but Dr. Light catches him. Wily is able to steal the plans after knocking Dr. Light down, and goes off to what is apparently an abandoned area, and modifies the old robot prototype into Protoman.

Later, Dr. Light builds Rock and Roll, advanced robots with personalities, along with Ice Man, Guts Man, and Cut Man. Dr. Wily and Protoman go and steal the robots, reprogramming the later three robots as henchmen. Dr. Wily attempts to reprogram Rock and Roll at his lab later, but Rock decides to trick Dr. Wily. He tells Dr. Wily that Dr. Light also built "super warrior robots", and that if Rock and Roll are let go, he'll tell him how to defeat the robots. Rock uses this lie (Dr. Wily believing robots can't lie) to cause a distraction and escape with Roll. Dr. Light decides to reprogram and reoutfit Rock into Megaman, who from then on keeps the world safe. This tale is told in Episode 1, "The Beginning".

Throughout the episodes, Megaman thwarts Wily's various schemes, in a similar fashion to that of the "Super Friends", usually ending with Rush acting like Scooby Doo, a character in another television show.

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