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It has been sixth months since the end of Mega Man X1, and with the loss of Zero the Hunters have turned to X himself to be their leader. Proving himself to be capable, for he had defeated Sigma himself, X and his Hunters were in the process of exterminating the various Mavericks.
The story itself settles X at the beginning of a factory where Mavericks are located, and so you must, as X, battle your way through that first portion, getting the hang of controlling him and defeating the numerous weak opponents.
If you succeed in defeating this opening level then you'll get to face off against numerous other stages, each one with their own boss, and watch as the story unwravels before your very eyes.
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Fooling around on bikes.
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Charging up.
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Charging up again.
