The year is 21XX. Reploids are commonplace now, after Dr. Cain rediscovered Dr. Light's old lab and based several designs off of Dr. Light's original, called "Mega Man X". X, meanwhile, has joined the Maverick Hunters, and works with unit leader Zero under the command of Commander Sigma. It is their job to terminate reploids who have become violent.
In the 26th century, humans discover a humanoid race living on the distant world GO/7498/2, a dark-skinned, golden-eyed people who seem to eke out a primitive, carefree existence. However, a scout team from Earth discovers that there is more to them than meets the eye--they live in symbiosis with vicious reptilian parasites, and the Terran scientists have upset the delicate natural balance.
In the year 2200 an interstellar war is held where the weapons most frequently used are the psychic capacities. The hero, Zero, son of an earthling and an extraterrestrial, the prince and last survivor of a clan of magicians. He will fight against the army of the Manjidara empire, whose forces are such as its head ambition to control the whole universe.