The problem with the X-Men franchise is that eventually, the underlying civil rights metaphor has to resolve itself. It would be like writing a story about Martin Luther King where he works for 80 years to get equal rights for African-Americans but nothing ever comes of it. One of the biggest problems is the presence of Magneto, the group's arch-enemy. Writer Grant Morrison attempted to deal with it in his epochal run on the series, finally ending the villain's life (after he killed Jean Grey again, more on that later).
Of course, that couldn't stand, so an absolutely insane editorial retcom occurred almost immediately after Morrison's last issue, where it was announced that the Magneto wasn't Magneto at all, it was a Chinese mutant named Xorn. Xorn, if you'll remember, was Magneto's cover identity in Morrison's run, which basically makes the whole thing the worst plan ever.
