Two hundred years have passed since the events in the Mega Man Zero series. Humans and Reploids have decided that the best way to stop all the bickering and wars that keep breaking out between them is to merge themselves. This was accomplished by adding cybernetic parts to the humans and assigning artificially limited life spans to the Reploids. So now, there is no real difference between a human and a Reploid; they’re both the same.

Unfortunately, this does not seem to have helped with the Maverick problem.

Before her death, Ceil and her team discovered something called Biometal. These mysterious talismans contained the Cyber-elf spirits of Reploid heroes—and villains. By studying Model W, Ceil was able to create Model X and Model Z. She knew that only certain people known as the “chosen ones” could utilize the Biometals. So she left a message for the chosen ones that would eventually end up using the Biometals she created, warning them that the Biometals gave their users the power to either save the world...or destroy it.

Years later, Ceil’s sister Prairie created the Guardians, a small army designed to protect people. They discovered the Biometal and various data disks left behind by Ceil.

Meanwhile two of the chosen ones, Prometheus and Pandora, appeared on the scene and began to cause their own brand of havoc. As far as these two were concerned, all of the chosen ones, or “Mega Men” as they came to be known, were destined to fight each other until there was only one left standing—who would then be the one to control (or be controlled by) the ultimate Biometal.

Yet, at the same time, the self-proclaimed “Sage Trinity”—the overrulers of the world’s new tyrannical federated government that formed after the war between the humans and the Reploids—worked behind the scenes to further their own desires...