Geological / environmental event
Smoke and ash choked the sky.
The smoke, ash and noxious fumes from the Earth's nuclear destruction fill the sky, plunging the world into countless years of constant darkness. This was a massive blow to the world's ecology and caused fundamental changes in the surviving flora and fauna. Most humans stayed in their shelters for most of this time as the environment was still to hazardous to support human life. Those who ran out of supplies and were forced out of their sanctuaries were changed forever by the brutal evolutionary forces.