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Waking from a century-long sleep, Zero encounters a mysterious young girl named Ciel. After saving her life from a platoon of deadly soldiers and a giant golem, he realizes he has lost his memory. 
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Ciel informs him that his name is Zero, and that long ago he was a famous fighter of justice, protecting humanity alongside X, the main character of the “Megaman X” series. X has since turned evil, however, and as ruler of the only heavily populated area on earth, Neo Arcadia, has deemed all Reploids (sentient robots) to be inferior citizens. Due to an energy crisis resulting from a lack of E-crystals, X made the call to “retire” scores of innocent reploids for the good of humanity. Ciel is leader of a small band of reploid fighters, though she is human herself, who strive to eke out a living for themselves whilst defending against the constant onslaught of Neo Arcadia forces. They’re on their last legs, though, so as a desperate measure Ciel set out to find Zero, the legendary hero.
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Moved by Ciel’s compassion and pleas, Zero agrees to help fight for the resistance, and as such begins a campaign of his own. He destroys disposal facilities, captures power plants, and faces the very generals of Neo Arcadia itself (Harpuia, Fefnir, Leviathan, and Phantom) in one-on-one combat. 
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After a particularly brutal attack, however, Ciel reveals two shocking facts: it was she who created X, and that X is mearly a copy of the original. At that very instant, a mysterious dataform warps in, instructs Zero to “terminate that copy of me”, and provides him with the coordinates to the very core of neo arcadia.
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Wasting no time, Zero transfers into the sanctum, and through many fierce battles and an ascent into space itself, arrives at the neural center of the Oppressive Utopia. Facing the Generals once more, Zero manages to rise to victory once again, with “Hidden” Phantom sacrificing himself in a futile attempt to stall him. d. Though excessively powerful, X is eventually defeated. With his dying breath, X initiates a self-destrucFinally, Zero arrives at Copy X’s lair and begins an intense battle with the replication of his erstwhile frient, and though he survives, Zero is left stranded in the middle of a desert. 
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Wasting no time, Zero transfers into the sanctum, and through many fierce battles and an ascent into space itself, arrives at the neural center of the Oppressive Utopia. Facing the Generals once more, Zero manages to rise to victory once again, with “Hidden” Phantom sacrificing himself in a futile attempt to stall him. Finally, Zero arrives at Copy X’s lair and begins an intense battle with the replication of his erstwhile friend. Though excessively powerful, X is eventually defeated. With his dying breath, X initiates a self-destruct, and though he survives, Zero is left stranded in the middle of a desert. 
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The Dataform reappears, revealing itself to be the original X in Cyber-elf form, and while apologizing for being unable to help, implores Zero to continue fighting and see that justice prevails. Gazing out across the endless dunes, Zero sees thousands of foes waiting for him. Steeling his resolve, he dashes forward into a new day.