Villains saving the world from the heroes

An overall story idea I had recently: A supervillain trying to infiltrate the headquarters of the not!Justice League discovers they’ve been replaced/body jacked/whatever by aliens.  The aliens are trying to get to as many superheroes and authority figures as possible as part of a covert takeover of Earth, but have been ignoring the villains, so now the fate of the world is in the hands of the not!Legion of Doom and their allies (or at least those who haven’t already thrown in their lot with the aliens).  Obviously people aren’t going to believe them about this, and the world is largely against them at the best of times, so it’s guerrilla warfare time.  I honestly don’t have much beyond a framework at this point, so questions/comments/suggestions would be appreciated,

I tend to prefer the crueler superwomen, so a story that focuses on a villainess (or several) instead of heroines could be fun. Seeing the difference in the approach villains would take on things like interrogating their prisoners, or deciding whether or not to free the heroes to help them fight the common foes could be interesting.

It is a good notion for a story. It needs more detail and depth but you knew that.

I like flipping the roles around. After all many villains are just heroes from another place. Maybe, a North Korean or Russian villainess realizes she has bigger problems.

Of course, even a psycho villainess might have her own selfish reasons for fighting. Why not divide things up with the aliens?

Janelle(Kiraling) and the reformed Arions show a more complex possibly diabolical side of villains.  They don't always have to be unspeakably evil.  They can subjugate and destroy competing villains or corrupt officials when it suits them or serves some greater purpose.  To many getting rid of one set of villains might be seen as heroic until the final purpose is revealed or exposed.  

If aliens are trying to take over the planet and then depopulate it then it would make sense for villains to fight for survival,  maybe once they realize they are also in the crosshairs.