We could have a kinda mix between cart's idea and slyph's ideas, suppose the US declares indefinite martial law until said otherwise, prompting a civil war as I'm assuming some Americans would be pretty PO'd about it. Also, other countries would send aid/support to their choosing, so it would be like a cold war type of thing as well.

Or, like Slyph said, have a town where all the supernaturals are rounded up and dropped off at, which is cordoned off from the rest of society, kinda like with new york in the crysis series, and basically have all your rights violated.

I guess if slyph really wanted to, the government forces attempting this could go all nazi and decide leaving new york to the supers wouldn't really be very cost efficient.Also, just like in crysis, there could be outside help. It could be from just different agencies or from all countries. Cept there won't be no nanosuit to save the supers...