After Zero turned evil after the previous game, Maverick activity has taken an uptick as he and Sigma make their plans to finally conquer the world. As X struggles to keep the world safe, help arrives in the form of another version of Zero...the Zero from the Mega Man Zero era. Both allies and enemies from the future are seeking to use the current events to change history and X must work with these new friends to stop Sigma and hopefully save the present Zero.

After Zero turned evil after the previous game, Maverick activity has taken an uptick as he and Sigma make their plans to finally conquer the world. As X struggles to keep the world safe, help arrives in the form of another version of Zero...the Zero from the Mega Man Zero era. Both allies and enemies from the future are seeking to use the current events to change history and X must work with these new friends to stop Sigma and hopefully save the present Zero.