Thomas Light and Albert Wily graduate MIT, Wily as Valedictorian of his class; Light as Salutatorian.
Light, while manufacturing industrial robots from his lab in upstate New York, begins working on prototypes for more advanced artificial intelligence. He consults Dr. Wily, who has been contracting his services out to the U.S. Government, with limited success; Wily's designs are considered too aggressive to be practical.
Drs. Light and Wily have made enormous progress in their AI designs. Dr. Light begins to integrate the new designs into his latest batch of robots, crediting Dr. Wily for his help. Wily accepts Light's gratitude, but numerous failed contract negotiations over the past several years have started to make him resentful of his counterpart.
Dr. Light asks permission from Dr. Wily to make some of their programming methods public domain. Dr. Wily agrees, then bitterly regrets it due to his ego.
Light and Wily begin design and construction of a single humanoid robot to test their latest experimental AI with; they designate this design a Master Series human replica android. Dr. Wily becomes aggravated as his robotics business flounders, overshadowed by Dr. Light's. He declines Light's offer of full partnership in LightLabs, Inc.
Construction of the prototype Master robot, designated Blues (and nicknamed Protoman by Wily), is completed by mid-June; the first two attempts to activate him fail due to a fault in the guidance system. Wily is gently admonished for overlooking it, and he fumes to himself in response. The International Robotics Commission is formed late in the year.
Construction of two production-model Master robots begins. With the Master Series' design specifications complete, the doctors also begin conceptualizing two prototypes, a male and a female, with which to test a theoretical free-thinking AI design modeled after the human brain. They are codenamed X and Zero.
Wily abruptly leaves, embittered to the point where his resent for Light has consumed him. He takes many of their collective designs, Blues, and the half-finished Zero with him. Light finishes the production-model Master robots a few weeks later, naming them Rock and Roll. Domestic models designed to look like children in their early teens, Rock becomes a lab assistant to Dr. Light and Roll is tasked with tidying up Dr. Light's home and office for the first time in anybody's recent memory. Work on the prototype X is shelved for the time being, but continues sporadically through the following years as Dr. Light studies artificial intelligence.
Light creates six more Master robots for industrial use. Days after their creation, Dr. Wily breaks into Dr. Light's lab with a combat-modified Protoman and steals all eight of the Master robots. The six industrial models are reprogrammed for combat; Rock manages to free himself and escape with Roll before Wily can do them any harm. When Rock later volunteers to retrieve the other robots from Dr. Wily and keep them from harming anyone, Light relucantly modifies him into Mega Man. Mega Man then goes on to stop an attack on New York by the other Master robots; Wily escapes in the confusion.
Wily's grievances against Light devolve into megalomania and he carries out several attacks with his own combat-oriented Master robots. In his fourth attempt, he kidnaps the daughter of Russian roboticist Dr. Cossack, threatening Cossack into attacking Dr. Light with his own series of robots. Mega Man dispatches them and learns Wily is the mastermind behind the attack. Mega Man helps Cossack rescue his daughter, thusly foiling Wily's plans. Wily escapes again. Protoman is recovered by Mega Man and taken back to Dr. Light.
Wily is captured by Mega Man and imprisoned; however, a hidden set of Wily's Master robots is activated after six months, and they proceed to break him out of prison. While trying to stop these robots, Mega Man is confronted by a HRA calling himself Forte. Though Forte claims to have been trying to stop Wily from escaping, he later enters and destroys Light's lab, revealing himself to be one of the failsafe Master robots. Mega Man defeats Forte and attempts to kill Dr. Wily after locating him, but shuts down due to behavioral programming installed by Dr. Light. Wily escapes, surprising nobody.
Enraged at a string of failures, Dr. Wily begins altering the still-incomplete Zero into a battle machine which he hopes will be able to destroy Mega Man. About halfway to completion he realizes that Zero's experimental body and neural hardware have still never been tested, and shelves her to begin working in earnest on a Mk-II Zero using the original's design as a reference. At the same time, Dr. Light is nearing X's completion, though he's altered the robot's design significantly, incorporating numerous elements and ideas learned from working with/on Mega Man for twelve years.
X is completed late in the year, but Dr. Light hesitates to bring him online, uncertain of the new AI's stability and fearing whether the world is ready. A lengthy automated program is prepared with which to put X's brain to the test, guided by an AI simulation of Light himself. Dr. Wily completes Zero around the same time, and proceeds to send her to Westchester, where she murders anyone who gets in her path en route to Dr. Light's lab. Mega Man ultimately fails to stop her, ending up torn into several pieces and deactivated. Dr. Light sends Protoman and Roll away, staying behind to secure X. Unlike Wily, he finds himself unable to escape.
Zero later relays a cryptic message from Dr. Light regarding X; Wily immediately sends her back, but as she arrives she's confronted by Protoman and Kagemaru, a cyborg created by Japanese roboticist Nobuhiro Takagi. The pair drive Zero off, Kagemaru and Zero taking heavy damage. While repairing her, Wily installs a computer virus in Zero designed to damage X's mind and turn him into a killing machine. Zero leaves to respond to an intruder before Wily can finish, which turns out to be Kagemaru; while Zero is distracted, Protoman kills Wily and sets off demolition charges to bring the fortress down on top of Zero.