I'll just start throwing out cool comic book plots for brainstorming!
-Magneto can have a whole world-dominating master plan of releasing a huge EMP to destroy probably at least the tri-state area's electrical grid, so huge blackouts, riots, etc, and thinking he was weakened by it, the X-Men go to stop him. Magneto tears out Wolvi's skeleton, which makes Xavier so mad and vengeful (although I'm sure he'd try to justify it by saying he had to), that he wipes Magneto's mind!
This arc goes on to have Onslaught unleashed in Xavier's mind, but we wouldn't have to go all the way there. Although a bit of it might be interesting! Traces of Magneto's mind in Xavier's.
-One of the mutant-hating/loving countries? Genosha or Asteriod M or something? Could have internment camps or mutant slaves or gladiators (another comm did this and was pretty successful; I know at least one or two people from there!). A mutant utopia would be a little boring, I guess.