Here's the VERY basic idea.
Modern setting. People with powers are very rare, and when they do appear for any reason they are quickly pressed into military service to their country.
A branch of the U.S government devoted to study of metahumans and the secret history of the earth. They discover a strange alien device which they think guided earth's evolution. They take it to a lab in a small town in, say, Vermont, and begin to run experiments on the device.
But something goes wrong. The device releases a pulse over the town, mutating everyone and everything in it. Where once the metahuman population was in the double digits, there are now hundreds.
Naturally, this won't do. A day later the government carpet-bombs the town, locks it down and capture or kills any surviving mutants in the town.
But in the day between the pulse and the assault by the government, many mutants escape into the country. Most flee to a much larger city for medical attention, but find government agents waiting for them. They gather together and head underground, trying to figure out what went wrong. The media and surrounding population are freaking out, trying to figure out why their government decided to wipe out an entire town.
Some mutants manage to escape their captors, and bring word to the underground community that the device is being held in the city above. A small faction gathers together to retrieve it. Maybe if they can get the device, they can turn themselves back into normal humans... or give themselves even more power.
That's my idea in a nutshell.