Unlike Mega Man Powered Up, Maverick Hunter X is a reboot to the X series that has many changes to the story that completely disconnect it to the original timeline. It was the intention of Keiji Inafune to completely redo the first six games of the Mega Man X series, but this project was discontinued due to poor sales of Maverick Hunter X.
These are some examples of the continuity with the rest of the series being ignored:
Dr. Cain discovered X many years ago (as opposed to months), and is artificially extending his life via mechanical support to oversee the Reploids. He also fears he does not have long to live. Towards the end of The Day of Sigma, a missile also destroys his home in Abel City - with him inside it (although it is left ambiguous as to whether Cain had actually died or not).
Vile's story, barring his flashback to Sigma's release of him from his cell, is merely considered a "what-if" scenario, as it conflicts with X's game. However,...
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