Pharos said
But two thing has always questioned me. Why did Doctor Light create him in the first place? And What happened to Megaman?
Hm....let's see. Actually Dr. Light created the original Megaman first. I think that Megaman was a mechanoid. Later, before the start of the X series, either Dr. Light updated the original Megaman and converted him into Megaman X, or he built another robot, I do not know which is right. Megaman X, unlike the original Megaman, is a reploid and the very first reploid to walk on Earth. If there's nothing mentioned by the Capcom staff about the original Megaman in the X series, then we could perhaps guess that he has been converted into Megaman X. Our guesses may not be right.
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If you look at the clues left around Zero was alive during Megaman series and also active before X was finished.
Secondly Zero was still maverick during the X series when he first appears.
Yes, Zero was still alive. X passed away but I think he probably became some kind of cyberelf and he could still help Zero keep on fighting. For those of you who do not know how a dying reploid can become a cyberelf, see the ending in Megaman Zero 2.