'X-Men: The Last Stand' continued:
The next scene which presages the movie's principle conflict is that of Warren Worthington Jr. discovering his son attempting to file off his wings--this being 'Angel'--and takes place about ten years prior to the current setting, and probably ten to twelve years after the meeting of Charles, Eric and the Greys. This leadup builds to the 'present,' wherein Mystique is captured after breaking into the Department of Agriculture and stealing documents referring to a cure for the mutant x-genome that seems to be responsible for the mutations.
When it comes to learning, the Department of Homeland Security places Mystique and several other high-priority mutant prisoners into moving prisons (a semi-truck with a police escort); in the hope of being able to prevent Magneto from teaming up with them. At the same time, the 'cure' is shown to be from a young mutant boy named Jimmy (a.k.a. 'The Leech'), whom Worthington Labs has been busy trying to isolate and recreate his (Jimmy's DNA).
The principle considerations that this places is: First what is the importance of being true to oneself? Throughout the movie, there is a recurring conflict between doing what one wishes, and doing something under the influence of others. At the same time, as represented by Charles; there is also a recurring theme of 'With great power comes great responsibility,' a line first muttered by Ben Parker not long after his nephew Peter turned into Spiderman. And Charles' importance in the mutant movement--despite the disagreement between he and his friend Eric/Magneto--is never more noticeable nor more missed than after Charles' death at the hands of Jean Grey (or more appropriately, her alternate personality, 'The Phoenix'), which both Eric and Logan witness at Jean's house. It is this importance that comes out between Magneto and one of his allies--a former student and friend of Bobby the Iceman, 'Torch':
Torch: "You know, I can't see why you're so upset of Xavier's death... hell I'd have killed him myself, if you had let me..."
Magneto: "You fool! Charles Xavier has done more to progress the rights of mutants than you could ever imagine..."
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