That, or let another Megaman franchise cannibalize it, like how original Megaman did to the X series by revealing that X was the original Megaman all along, and that Zero was Dr. Wily's creation.
Was that in X4?
For X, it's never really stated (although, you gotta think on the "where's Mega Man" question). For Zero, it's hinted at and then outright confirmed in X8
when Sigma states that Zero was the original carrier of the Maverick virus. The mad doctor in Zero's dream in X4 looks quite a bit like Wily. His rant about "destroy his enemy" is probably referring to either Mega Man or Dr. Light (and potentially X; time is never stated) and Wily's W(TM) appears when Zero has that massive headache in the Sigma vs. Zero flashback. In X2, Sigma states that Zero was the last of "the doctor's" creations. That doctor being Wily.