After Sigma's fifth defeat and Eurasia's destruction, the earth is greatly damaged.While the maverick hunters and reploids repair the earth, the human wait underground.In an successful attempt to save the earth, zero sacrificed himself to destroy Eurasia before it hit earth. Although the Sigma Virus was thought to be destroyed, a reploid repairing a building goes berserk and X is sent to check it out.Little does X know that this virus was caused by Zero's body and its destruction.A reploid named gate has been infected with a form of the maverick virus that has been combined with Zero's DNA found at the crash site of Eurasia. Using Zero's DNA he makes new more powerful reploids to take over the earth. X now sets out to stop Gate, but always listens for Zero's signal...