A hundred years after the fall of Sigma, Maverick Hunters X and Zero have vanished from the view of the public and have become mere legends. Humans and Reploids find themselves at war as the humans have decided to stamp out all of the robots that caused the wars of the past.
Two factions emerge: some Reploids continue to serve the humans, even though the humans are in the process of systematically destroying most of the Reploids. The rest of the Reploids have fled, creating a Resistance Force in an attempt to save themselves from annihilation.
Ciel, a human scientist, joins a group of these Reploids, who have constructed a Resistance Base as their place of operations. By studying Cyber-elves, Ciel hopes to develop a new source of energy that she intends to use to bring peace between the Reploids and the humans. Until then, they fight.
When the real X appears, it is in the form of a Cyber-elf. His body is sacrificed in an attempt to imprison the Dark Elf, the source of the Elf Wars that nearly devastated the world years ago. Now X serves primarily as a source of guidance, though he tends to give as little information as possible, revealing things incrementally.
Meanwhile, Dr. Wiel, a scientist banished from Neo Arcadia for instigating the Elf Wars using a robot known as Omega, returns with a vengeance to attempt to accomplish his goals once and for all. He takes over Neo Arcadia and makes prisoners out of the humans as much as he wages war against the Reploids.
For more information, check out the various game hint pages for details about the plots that this history lacks.