The story of the X series is a bit more vague than the originals, if only because so much is unmentioned or not clarified in the games themselves. Sometime during the original series, Dr. Light designs the next stage of robotic evolution and it comes in the form of Megaman X. X is a robot who can think for himself and make his own decisions. This technology was highly dangerous and would require at least thirty years of diagnostic testing. Dr. Light, who was in an advanced age at this point, knew that he would not live long enough to see the testing completed. So, he designed a special capsule and sealed X in it.

Over time, Dr. Light's Laboratory was somehow destroyed. But during an excavation project, a Dr. Cain unearths the great scientist's chambers and with it, the capsule containing X. With the testing having been completed, X emerged. Fascinated by Light's genius, Cain went forth and designed a new series of robots, called Reploids, based on the design of X.

However, since the robots could think for themselves, their actions would have to be repressed if they endangered humanity. In order to police this Maverick activity, Cain formed the Maverick Hunters and named a Reploid, Sigma, as their leader.

All was not to be peaceful, however, for one day Sigma decided to turn against the humans. Defecting from the Hunters, Sigma becomes the leader of the Maverick resistance, claiming that he will be the bringer of the true destiny of the Reploid race. Faced with an emergency, Cain had X go out to fight Sigma. X is paired with a crimson Reploid, named Zero, in battle.

For most of the series, Zero's origins are uncertain. The enigmatic lines about how Zero must one day turn against X aren't elaborated upon until X4, when we learn that Zero's creator was none another than the mad Dr. Wily.

So here is where the vagueness comes in, because how do Zero's true origins relate to Sigma? Did Zero destroy the original Megaman? Why is Zero constantly rebuilt time after time again? And perhaps the more pressing question whatever became of Dr. Wily?