The Laundry Files by Charles Stross is about a top-secret British intelligence agency charged with managing all things supernatural.
The sci-fi twist is that magic is basically applied math, and as computing becomes more ubiquitous, more and more stuff starts leaking over.
Think a joke-cracking IT professional evolving into James Bond as he fights the supernatural, and you've got The Laundry Files.
Bob Howard from Capital Laundry Services shows up, the books are confiscated and everyone forgets it happened. This probably kicks off an interesting adventure involving time travel, where we learn that the Deep Ones actually opened the first book store some time during the mid-paleolithic.
Charlie Stross's Laundry series. Sci-Fi -> Lovecraftian Fantasy in an action/spy thriller framework.
Lois McMaster Bujold's Vorkosigan saga.