Set an indeterminate amount of time after the events of Mega Man X4, a new plot to destroy the Maverick Hunters is hatched by Sigma, who has been revived again (as in X4, it is unknown who revived him or how). Sigma, after conducting research on the origin and design of Zero, decides to discover how to unlock Zero's true power, hopefully destroying X in the process. Sigma attacks the Maverick Hunters directly, intending to lose. When he does, he spreads the Maverick virus across the Earth, throwing it into chaos. Meanwhile, a Reploid mercenary named Dynamo is hired by Sigma to make the space colony Eurasia collide with Earth. The Hunters have only 16 hours to stop the collision.

In order to prevent Eurasia from striking the planet, the Hunters pursue two options of attack. The first option is to fire a powerful cannon called Enigma at Eurasia, hopefully vaporizing it. If the Enigma shot fails, the second option is to launch a space shuttle and pilot it into the colony, destroying it. To maximize their chances, X and Zero are dispatched to collect parts for the two devices. The necessary parts to upgrade the Enigma and shuttle are held by eight Reploids and Mavericks), and X and Zero must defeat them to claim the parts. Further complicating matters, Dynamo repeatedly attacks the Hunters' base during the course of the game, forcing X and Zero to waste valuable time fighting him off. (Hint: the last standing member of Repliforce, The Skiver is present in the game. By destroying him, the Repliforce's completely wiped out.)