Ok, reading through, here's the current idea you guys seem to agree with on the whole. If you'd like edits I will do so.

There's a super villain who comes into contact with an alien race. They convince him that if he gives them the coordinates of Earth, they'll take it ovet and allow him to rule it. The aliens come to Earth and begin tbiet conquest, immediately after making a public spectacle of killing the aforementioned Super-villain in Times Square. The superheroes mobilize and syart destroying portions of the alien fleet. They realize that using the fleet on humanity is more trouble than its worth and release a prototype virus, so they have time to rally thier forces. The virus decimates the already crumbling humanity,  leaving only a small amount of the population left. Some of these survivors are ex-heroes, and a small amount(I mean, REALLY small) developed powers as a result of the virus. Only (not sure of exact percentage. 5%? I dunno.) of the population remains, waiting for the aliens to return.

Everyone on board with that? Also, terribly sorry for any spelling errors, I'm on mobile.