Taking place a few hundred years after the Mega Man Zero series, Mega Man ZX begins after the fighting between humans and robotic people called reploids has ended, and the two are coming together to share technology and live in harmony. Mavericks, a rogue band of disgruntled reploids, are ruining the peace by attacking outer colonies of humans and robots. The heroes of the game are Vent and Aile, two young adults bent on revenge after the Mavericks attacked their transport ship, killed all their friends, and left them stranded in deep space. After absorbing X Biometals into their bodies, Vent and Aile are able to transfigure into a Model X form of reploid, complete with super powers.

After discovering the crazy new abilities they possess such as a long-range buster shot, dashing, and wall kicks, Vent and Aile explore an open map, completing story missions and side quests, defeating enemies, and collecting the Biometal they leave behind. If undamaged during the fight, the Biometal can be used to transform into different reploid models such as a Model HX or a Model LX, and will open up new skills and abilities as well as make previously unreachable areas available for exploration. If the Biometal is damaged, players must repair the item before using it. The lower screen of the DS is used to organize and apply Biometals and other items or abilities gained during gameplay. The touch screen provides information about the metals, pinpoints enemy weak spots, and creates and combines weapons.