When fumbling around an old thread, I found a reference to work by a Charles Stross... who, incidentally, is also the gentleman who contributed Slaadi, Githyanki, Githzerai, and Death Knights to D&D. The story referred to in said thread was a sort of Delta-greenish yarn about an alternate history cold war where a CIA agent is striving to deal with a Russia armed with shoggoths and Iraq is trying to open a gate to another world.
(It's available free online here
I found out I already own this story in a collection I have, which has another one of his stories, Antibodies, about a group of agents from an alternate reality trying to prevent a cross dimensional takeover by AIs when a technology singularity occurs.
Why has he flown beneath the spycraft fan radar? His stuff sounds like great fodder for Spycraft games, especially of the Shadowforce Archer or Fragile Minds persuasion.