As the public outcry against the few Maverick incidents becomes too great to deny, the government steps in, and under the advice of Dr. Cain, forms an elite military police organization called the "Maverick Hunters". The Hunters are to capture or disable any Reploids that pose a threat to humans, provide damage control at Maverick uprisings, help with disaster recovery, and perform other tasks as needed. To lead this group, Cain designs a very advanced Reploid, thought to be immune to whatever defect causes Mavericks. This robot, named Sigma, heads the Hunters for some time before ultimately becoming a Maverick himself, alongside the vast majority of the other Hunters. Sigma seizes control of a small island, driving out all human occupants. Claiming that the humans are inferior and that they are limiting the growth and potential of Reploids, he calls for his followers to begin a massive extinction effort. X, guilt-ridden at having helped design such a dangerous race, joins forces with the only other remaining Hunter, Zero, in order to stop Sigma at any cost.