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.
Whether the Enigma and shuttle succeed or fail is randomly determined by the game, although the Enigma's chances of working successfully are low even with all its parts, while the shuttle has a much higher probability of succeeding assuming all of the parts are collected. If the Enigma succeeds, the Hunters can proceed to hunt for the cause of the virus without fighting the remaining Mavericks (though it is still recommended to do so, in order to get weapons and items from the Maverick). If the shuttle (piloted by Zero) succeeds, the hunt for the cause of the virus begins as well. If the shuttle fails or if your time expires, the colony crashes, nearly destroying the planet; Zero then is infected by the virus and goes Maverick, removing him from the game as a playable character.
In either case, once the location of the virus' origin is discovered, the Hunters must investigate it. X (and Zero if he's still playable) penetrate a bizarre underground fortress, based on levels from previous games and featuring enemies from the distant past. Finally in the third stage of the fortress, X and Zero cross paths, and mutual suspicion and mistrust leads to a duel between the heroes (which had been foreshadowed ever since the end of Mega Man X2).
After the duel, the story diverges slightly. If Zero went Maverick, then he sacrifices himself to save X from Sigma, and X continues on alone to get revenge on Sigma in the final stage. If Zero did not go Maverick, he saves X and himself from Sigma, and both heroes have a chance to confront Sigma in the final battle. There are three possible endings for the game; X has two and Zero has one.
If Zero went Maverick, X defeats Sigma, but is badly damaged. He recovers, but all of his memories of Zero are deliberately erased by a mysterious person. This is considered the "bad" ending, and is treated as non-canon.
If Zero did not go Maverick, Sigma decides to make the Hunters' victory for naught by taking them down with him. X tries to save Zero but is ambushed by Sigma and both Hunters are critically damaged. Zero manages to finish Sigma off, then the endings diverge again. If Zero defeated Sigma, he reflects on his origin and life before dying. If X defeated Sigma, he inherits Zero's beam saber and continues to fight as a Maverick Hunter. This is considered the "true" ending.
It is interesting to note that though the manual says that the Repliforce was wiped out, the Skiver has the Repliforce symbol on his head, and the Repli-air force is mentioned as still being there.
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