Taking place a century after 'Mega Man X5', the world was at peace. However, Mega Man X started to terminate innocent reploids to ensure there won't be any Mavericks attacking the innocent. In a desperate attempt to end the conflict, a human scientist named Ciel searches for the legendary Zero. Zero is shortly awakened by Ciel, but has a memory loss. Zero must help the newly formed Resistance forces, defeat X and find out his true identity. Little does Zero know that the X ruling Neo Arcadia is a copy created by Ciel shortly after the real Mega Man X's disappearance.