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Megaman X is called to a cell owned by the Maverick Hunters in New York City an asked about "Robotizers", although X denies knowing their locations. Meanwhile, Zero and Axl are continuing their expidition to the Maverick Generation Factory from the TV series!. After Axl destroys the generator the building collapses and Zero is almost killed by a maverick. Dr. Cain tells them that a large maverick is attacking Boston and they head off. Meanwhile, a human Maverick Hunter, Sympha, leads his group into the ruins of Light Institutes.
At the ruins, Sympha finds the Robotizer and attempts to activate it, turning himself into a Reploid in the process. He kills the rest of his group and sets his sights on destroying the one who did that to him: X. At the MH2Q, Megaman X is imformed about Sympha and is ordered to a safehouse; but when they leave, Sympha and his new reploid group attack. During the battle, Sympha sneaks into the building and projects a pre-recorded video of him announcing his war onto a building. According to him, and reploids that want to join must just say "Sympha-size".
Megaman X realizes that Sympha is at the Reactor and heads to the Core, arriving when Sympha has finished charging. Before X can intervene Sympha steals a Si-Cycle and races to the Blackmarket, trailed by Megaman X. At the Blackmarket, Sympha trades the energy for the machine, but X destroys one of the pipes and the auctioneers disolve. Sympha flees and X traces him. They fight to the large window and X destroys both pipes, overloading Sympha with Human and Reploid energy. He malfunctions and falls into the canyons below.
As Zero and Axl head toward Sytha City, they see Symphas remains in the river. Zero scans it and finds that it is both human and reploid, dubbing it Humanoid. Zero and Axl carry it, talking about their discovery.