Hundreds of years has passed since the war of humans and Reploids. However the Outer section of the world is terrorised by fierce Maverick while Inner area is peaceful. Serpent Company, a company providing energy to the Inner area and defending the peace against the Maveric, is on a quest to the Outer region as they discover relics of ancient technologies. These Biometals are transported by Girouette Express and you'll take the role of either the male Vent or the female Aile who are employees of the company.
During the transportation of these relics, group of Mavericks attack to interrupt the delivery. During the fight Biometals are absorbed by your character and your boss Girouette tranforming the main character to Model X and Girouette to Model Z. The boss lends his power to his subordinate and the Model ZX is formed. The player is now in a mission to restore all the different Biometals and getting access to different Models, and to ultimately find out what the cruel enemies are and what they are after.
Mega Man ZX, for the first time in franchise history, includes a playable female character, Aile, as well as Vent the male employee. Each of the two characters have their own characteristics and the transformations to different Models extend their abilities.
The game takes use of both of the DS dual-screens, using the top screen for action and bottom for information such as hidden items.