What happened in the time between Mega Man and Mega Man X, and how they connect, has long been a source of mystery, speculation, and fan fiction about Zero murdering everyone. Is it possible any answer exists at all? According to Capcom, it does indeed, but they're playing their cards close to their vest.
Coming from The Reploid Research Lavatory, which has been translating answers to fan questions from the recently released R20+5: Rockman & Rockman X Official Complete Works:
Q03: Has what happened in the interim between the Rockman series and the Rockman X series been decided? Or is there no canon version of what happened?
CAPCOM: Of course there is such an outline, but don’t expect an official announcement of it. Players have always enjoyed using their imaginations to come up with their own conclusions, and we wouldn’t want to take that away from them…
However, has Capcom really been so quiet on the matter?
While of course nothing has been explained in detail, dots have been connected here and there. In fact, nearly three years ago when Rockman Zero Collection was coming out, Capcom of Japan posted a timeline that seemed to indicate the X series had its origins from the events of Mega Man 10:
At least 200 years ago The birth of X
When an incident occurred where an unknown computer virus came from space and causes robots to become violent and riotous, Dr. Light completed the battle robot “X” worrying about the future of Earth. Hypothesizing X could battle robots infected by viruses, he gave X the perfect virus counter-measure. Meanwhile Dr. Light developed a great number of armors, but this presented the possibility of X becoming a threat to mankind. To confirm the safety of X’s cognition program, Dr. Light sealed away X in an analysis capsule.
1XX years ago The birth of Zero
Zero was produced by Dr. Wily, who schemed at taking over the world. But he contained a flaw in his cognitive program that made him violent and unwilling to obey instructions, so Dr. Wily himself sealed Zero in a capsule.
Curiously, though, this timeline has completely disappeared from the Rockman Zero Collection homepage, so far as I can tell. Perhaps a recent retcon? But to what end? Mega Man 10 and the Zero Collection are basically the last new Mega Man games to be released (not counting Xover).
Anyway, though, you should definitely check out all of Kobun #20's great translations!
News Credit: GoNintendo