re: Can someone explain how Charles Xavier died in X-Men 3 but is in future movies?

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Was it one of those post-credit things that comic book movies like to do? B/c if that is the case, then yes, I didn't see that prat.

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Yes in part. There were a few scenes that set it up earlier in the movie as well. Charles was posing an ethics question to students:

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"His organs and nervous system work, but he has no consciousness to speak of. What if we were to transfer the consciousness of one person, say a father of four with terminal cancer, into the body of this man? How are we to decide what falls within the range of ethical behavior and what... (interruption)"

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Moira is seen with this man in a coma during the movie. Then at the end while the movie brings up the loss of Charles we see the comatose man awaken for the first time. The implication is that Charles found his way into this body.

(It turns out that this is actually charles' twin brother, having actually killed him with his powers in utero.)