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.
There was once an ogre mother who gave birth to human looking child. Instead of an ogre's horn, this child was born with a sword in hand called the Onigirimaru (Ogre Slayer). He has no name and is only referred to by the name of his sword. Though he appears human, he is pure ogre. Believing that he will become human once all of his kind vanished from the world of humans, he sets out on his destiny to slay all of his kind. Even now, in the mother world of Japan, he is still out there slaying ogres.
Due to a spacecraft malfunction, saleryman Ryu and his robot companion "MOS-01" crash land on the space ship/planet Gdleen. Ryu meets a cute Euredonian fairy called Fana and the two are soon entangled in a long standing war between the monsterous Babaress and the spell casting Miyorl tribes.