Oh, You're looking for Post Apocalyptic stories. Threre are a ton of those, enough that it's a category in "category search". There are 226 returns with that tag.
I thought you were keying on Muslim invasions, which is a less populous and not as popular a trope.
The top rated PA story on SOL is "Aftermath" by Al Steiner, although that ones a comet crash (Score: 9.35).
The second highest rated one is "Getting By" by Shakes Pere2b. That one has a bio-weapon depopulating the earth (Score: 9.10). It also has a highly rated sequel.
"Future Distorted" by Celtic Bard seems to match your wish list almost point for point (Score: 7.82).
There are a couple of the writers who post here (a lot) that write PA. I'm sure they'll be along to put in a plug their own works, I'm not as pamilair with their bibliography as they are so I won't mention stories any by them.
Oh Yeah. Puportedly the best PA/plague book in dead tree, available in most any public library is probably "The Stand" by Steven King.
My taste runs more to S. M. Stirling's 'Novels of the Change'.
John