After defeating Sigma in the last game, Axl has joined the Maverick Hunters for good. Unfortunately, Sigma's last few plans has greatly damaged the world. Now a project called the Jacob Project has been developed.This project's goal is to create a elevator to the moon where humans and reploids hope that they can explore space. To build this elevator, new reploids based on Axl's prototype body have been built.Even with the best anti-maverick programs avaible, some of them are going maverick, a state in which reploids lose control and attack senselessly. X, Zero, and Axl have been ordered to stop these new mavericks and thus defeat Sigma once again.