It's well known that Capcom can't write a plot worth a damn. They've tried, bless their hearts but Mega Man, especially Mega Man X has always been a textbook idiot plot, and Mega Man 3 is probably the most flagrant example. With Dr. Wily stated to have proclaimed himself a good person and teams up with Dr. Light, the question on everyone's mind no doubt is "Why does everybody somehow believe Dr. Wily's a changed man?" The answer to this question, it seems, is "Who cares? It's a video game. If you want story, go read a book or something. We're here to blow up robots and have fun.