In the late 22nd century, humans have commenced a construction of an orbital elevator to the Moon. A Reploid named Lumine was put in charge of the project. Lumine belonged to the new generation of Reploids, which were apparently unable to become Mavericks (i.e. turn hostile towards humans). Soon thereafter, Lumine was kidnapped by unknown assailants. The team of Maverick Hunters, composed of X, Axl, and Zero, must pursue the abductors and find what they were truly after. However, they will also have to deal with familiar enemies from the past...