I am looking for others’ recommendations for the best Spec Fic stories centered around covert organizations and their dealings/activities. Intelligence agencies, special units, black operations, etc.
Some examples that spring to mind are Special Circumstances from The Culture series and Section 8 from Star Trek.
You might like Laundry Files by Charles Stross. It’s focused around a secret government agency that deals with eldritch horrors (and tries to keep the public from finding out about magic).