Dr. Wily was Dr. Light's assistant until he became jealous of him. He then stole and reprogrammed the robots Cut Man , Bomb Man , Elec Man ,Ice Man , Fire Man , & Guts Man to enact vengeance on him and take over the world.
He sent the reprogrammed Robot Masters to attack the city, and later made a TV appearance claiming responsibility for the atttacks. Just when it seemed like nothing could stand in his way, one of Dr. Light's helper 'bots stood forward to be weaponized and upgraded. This helper 'bot was Rock , a peaceful robot who helped Dr. Light along with his sister Roll , Dr. Light saw the two, not as robots, but as his children, and he told Rock that although he didn't want this for him, he couldn't be prouder. Rock took the name Mega Man and set off to defeat the Robot Masters. Dr. Wily originally just saw Mega Man as just a small blip in his master plan, but he later came to see how powerful he was when he defeated all the robot masters. Dr. Wily had the robot masters rebuilt and set off (once again) to destroy Mega Man, but he talked them round and they rebelled against Dr. Wily. In one final confrontaion with Mega Man, Dr. Wily was defeated and arrested, screaming that he would get his revenge.
After being defeated by Mega Man, Wily was taken into custody by the police. Wily was still shocked that a little helper 'bot like Rock could be such a foil to his plans. While being relocated to another prison, Time Man freed Wily and he was able to escape. He then began his next plan, to eliminate Mega Man and conquer the world. He had Oil Man kidnap Roll to ensure that Mega Man did not come after him, however this only made Mega Man more determined too defeat him. Mega Man tracked down Wily's new hideout and (together with the robot masters and Agent Roslyn Krantz) entered in the hopes of defeating Dr. Wily. Dr. Wily attempted to reprogram the Robot masters, but to no avail, his new robot masters were defeated, and Roll rescued. If it were not for a clever trick with a hologram then Wily would have been arrested, however he escaped to fight another day.
Dr. Wily travels to ancient ruins and rebuilds the Mega Man 2 Robot Masters and builds new Mega Man 3 Robot Masters. He finds Shadow Man and incorporates him into his army. Blues also shows up and Wily weaponizes him while upgrading his power system. Blues is now called Break Man thanks to Wily suggesting that it represents his want to break from his past. During this time he somehow meets Ivo Robotnik(Eggman) and hatches a plan to merge worlds.