Megaman 10 confirmed

[Rob]

Zero dies again in X5 after Sigma covers th world with the virus and destroys a lot of the planet, and its found out that Zero is the source of hte virus and rather htan get infect he becomes much stronger
eventually zero and X fight eachother, either for stupd reasons or because zero absorbs a lot of virus and becomes his "true" self
Its revealed the plot was set up by Wily who informed Sigma of Zero's true self and Sigma sought to awaken that

Interesting thing about X5 that it was originally the end of the X series and would cut off into the MMZ series, infact if you get the ending with X when Zero went Maverick it actually hints at it, but they say "no not yet" and continued the X series from there. also MMZ4 had the same credits theme as X5 did.