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 and hatches a plan to merge worlds.