With the Alien angle you could go a few different ways:
1. Typical Invasion idea, but.....instead of full on invasion like ID4 (it would be way obvious and unlikely to be hidden or unknown to anyone) they orchestrated the war in order to weaken humanity - perhaps the tech difference wasn't enough to ensure a win*. The virus in this case may be their first attempts at altering the environment to suit their biology. Or it could be an unforeseen side affect of their weapons - which could end up being a way for humanity to fight back. (Mutations!! You gotta love 'em!!)
2. The aliens were here as passive (and not-so-passive) observers and were caught up in the conflict and decided to assist humanity. In this scenario, there would possibly be less alien tech out there and the mutation virus was developed as a quick solution to the massive radiation which WOULD have killed off (nearly) every living thing on the planet.
3. Like 2 above, only they had nothing to do with the virus or helping or harming (at least not on purpose), they are just scientists studying a lower life-form. The virus could be of human manufacture for whatever reason, or it could be just another experiment by the aliens.
4. There could be two (or more) warring alien species and they chose Earth to fight on so that they don't harm their own homeworlds as life sustaining worlds could be hard to come by and the species willing to harm their own is stupid in the extreme. (You even get a moral lesson with this one.
) This gives you the opportunity to develop different aliens, as well as the PCs to maybe make some allies. The virus could be because of any of the above reasons. For an idea on how the aliens got here see the book
The Last World War by Dayton Ward.
Hope these help, Rand.
*We (humanity of Earth) have lasers now, if the "Final War" occurs up to one-hundred years from now, it is not impossible that the average soldier would have an energy weapon. Not extremely likely, but not impossible.