Mega Man X is the titular main protagonist of the Mega Man X series and a supporting character in the Mega Man Zero series. While always planned to be a hero in the former series, he was initially planned to be the main antagonist of the latter series before being replaced by Copy X.
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Back when Keiji Inafune was first writing the script for the first Mega Man Zero game, he had planned for X to be the villain. Following Zero's death at the end of Mega Man X5, X builds a city called Elysium. However, as the city grew with him as the leader, he became corrupt with power and started declaring reploids a threat to the world. Meanwhile Zero is revived and learns of the atrocities that X committed. The game would have ended with Zero having to put down his old friend for good. However, along with the fact that X6 being produced while Zero's script was still being written, Capcom thought that having X as the villain would be a disservice to fans of the original series.
As such, in order to connect Zero with X6 and appeal to fans of the former series, the script was rewritten with X now as the big good of the Zero series and the villain being a replica of X.