Registration on the game, not just in the US but worldwide, was not aimed solely at mutants though it began with them as they were the most obvious. It was aimed at everyone with powers and was starting to include everyone who was not 'baseline human'. Were mutants supposed to register? Yes. Were aliens? Yes. Mages? Yes. Mutated and augmented? Yes.

Captain America was expected to register. So were the Fantastic Four. And Thor, Doctor Strange, and Iron Man. The definition of what was 'above normal' and a potential threat was constantly widening. Some started to argue that Olympic level athletes qualified as well as those with a genius level IQ. It was at this point that the pushback really began which eventually led to the shift in political power in the US.

While the Registration laws are no longer in effect and its proponents no longer control the White House or Congress, there are still politicians in office who supported it and still do. There are still citizens who supported it and want to bring it back. Prejudice against those with powers definitely exists, whether they're mutants or not. 'Powered', and for some people, 'above normal', has joined race, color, sexuality, religion, etc, etc, etc as a reason to discriminate against others. They're not the majority but they're there.

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