Last week Capcom-Unity invited fans to send in questions, ten of which selected to be answered by the mega man himself, Keiji Inafune. And word up to all you guys with that "What happened to Dr. Wily in the X series?" signature pic guys in our forum: go find some cute Pokemon or something 'cause you won't need those anymore. Here are a couple choice inquiries to Keiji: 1) Did Zero really "kill" the family between the events of the Classic Mega Man and X series?
KI: No, Zero did not kill them. According to the way I created him, Zero is not such a person--it is not in his profile.
6) What happened to Dr. Wily in Rockman X series? Are Dr. Wily and Dr. Weil the same person? Were they ever supposed to be?
KI: A large amount of time has passed between the classic series and Mega Man X. Dr. Wily had died in the interim but was brought back by the virus. Dr. Wily and Weil are not the same person. It is ironic though, because Dr. Wily created Zero, and Dr. Weil used Zero, but ultimately it was a copy of Zero's original body with a different mind that defeated him.
With one answer he blows away years of careful speculation. 'Course, I have a feeling the hardcore timeline fans will just find other stuff to ponder in its place. Check out the whole select of questions and answers here.
Edit: For archival purposes, we've added the post in its entirety to our Interviews section here. --LBD