Sounds like a setting that cries out for Charles Stross' "The Laundry", from his book The Atrocity Archives.
http://en.wikipedia.org/wiki/The_Atrocity_Archives
Charlie, being a good egg, has even put his novella "The Concrete Jungle", part of the Archives setting, online under a Creative Commons license. Enjoy.
http://www.goldengryphon.com/Stross-Concrete.html