In Zero's first mission, the human researcher, Ciel, recruits the legendary warrior to fight against the anti-reploid organization "Neo Arcadia". Together, Zero and Ciel create a resistance group and put a stop to the senseless aggressions from the NAO. Once again humans and robot reploids are able to live in harmony. But for how long? In this next mission, Zero falls prey to a trap set by Neo Arcadia’s newly, self-appointed and ruthless commander. His plan is to trick Zero and use him to wreak chaos between reploids and humans once again. But, can he succeed? Features:

Form Changing System - Depending on the player's style, Zero will gain new, latent powers. When Zero awakes these powers, his color and abilities will change. There will be different forms hidden throughout the game.

Link Battle – Players can use the original Zero to battle against friends via the Game Link Cable. Each stage offers a special link stage in which player's race against their opponents, collecting items and trying to be the first to escape.

Extra Skill Capturing - If the player can beat the level with an 'S' or 'A' rating, they will be able to use that boss's special skill on later levels.

Version Up – Mega Man Zero 2 features more types "Cyber-elves" (collectable characters that provide help to the player) than the original. Capcom has improved the interaction making them even easier to use. Players can now gain a large variety of "code names" and be wary of the numerous traps that await them.