Reference for anybody who might not remember what he is talking about:
http://www.mobygames.com/images/shots/l/412202-fallout-3-mothership-zeta-windows-screenshot-ruined-earth.jpg
http://fc05.deviantart.net/fs48/f/2009/220/e/7/Mothership_Zeta_4_by_allenrb2.jpg
On to the question though, I actually wondered the same thing when I first played through Zeta and came up with a few different possibilities:
1. Its some sort of strange meteorological anomaly caused by adverse conditions in the Fallout Earth's atmosphere (also SCIENCE!).
2. Its an area that was hit with an enormous concentration of nuclear weapons when the war occurred.
3. Some sort of distortion or illusion of some kind.
4. Other than that, perhaps some strange terra-forming experiment by post-war scientists (or pre-war) that went horribly wrong.
I'd honestly like to hear some thoughts on this as well. Seems like an interesting topic to discuss.