The bad doctor, Albert W. Wily. According to some sources, he was a close collaborator with Light until a lab accident damaged his mind. Possibly he always harboured ill feelings and one day gave in to them. Either way, once his ambitions had flared up there was no stopping them. He had to be recognised as the world’s greatest roboticist at any cost, his madness increasing as he went on. But always he had to contend with Light’s creations, especially Rock, and he always came up short.
Among Wily’s creations are the Robot Masters from Mega Man 2, 3, 5, 7, and 8. He is also responsible for reprogramming most of the Masters from other Mega Man games for evil. Other robots not of the particular “Robot Master” variety include the Mega Man Killers Punk, Enker, and Ballade; Reggae the Crow, King, the Doc Robots, various imperfect copies of Mega Man, and Bass (who serves as an antihero) and his partner Treble.
However, he considers his greatest creation to be Zero, who contained the double whammy of unstoppable killing machine and insidious computer virus to corrupt any robot. He must really resent that Zero turned against his destructive programming and began fighting the Mavericks he helped create.
While Light managed to live on in a limited fashion, Wily had his own means to survive through the following era. It is implied that the robots Serges from X2 (second image) and Isoc from X6 (third image) are partially Wily himself or at least closely linked. It’s not unheard of in fiction for someone’s personality to be converted into digital form and housed in a robotic body, and if anyone could figure out the means, Wily could. He would also have the inclination, being irredeemably sociopathic. Having said that, there have been moments of sympathetic portrayal for Wily, especially in the Classic days.
Undeniably a genius, Wily is nevertheless crippled by his jealousy of Dr Light and delusions of grandeur. He is arrogant and a natural manipulator, having mastered the art of deception. His narcissism extends to his creations, leading to a desire to prove his robots are better than Light’s, specifically hoping for Bass to outclass Rock and later Zero to X.
Dr Weil (fourth image) continues in the vein of Wily’s machinations in the Zero series, taking command of copy X and Zero’s original body as his tools. He has similar megalomaniacal tendencies and skills of deceit, managing to take command of the largest civilised settlement in the new world after the destruction he had wrought. His goals are to use Reploids as slaves and rule the world, not wholly unlike Wily, although Wily was shown to have some respect for his creations. Weil shares this respect only with Omega Zero, continuing the thread of Wily and Zero. There is no concrete link between the two aside from name and personality, especially as both are human.
Wily reappears in a way, as part of the Sage Trinity in the Biometal era. As Master Albert (fifth image) he rules the country of Legion with the other Masters, although it is unclear how directly this version is based on Wily. He has very strong links to Model W though, which implies more connection between Weil and Wily through the Biometal Weil is the progenitor of. Master Albert takes Wily’s ambitions to the extreme, wishing destruction and recreation of all the world with himself as its god. Meanwhile, he maintains a facade of cool calmness. He claims to be the master of the Model W Weil created, but it is unknown whether it is actually using him.
There is a minor character named Wily in Legends who shares a resemblance, but he is merely a friendly boatman.
Wily’s Network counterpart is Lord Wily (sixth image), a schemer in a similar vein with a jealousy of Dr Hikari’s work. In this case however, Wily is also a robotics expert, changing the dynamic as he is resentful over his technology being superseded by Hikari’s Network technology. He is not the primary villain in all the games, and even is redeemed in the end and resolves to help improve the world.