Star Trek: Utopia's Fall, Or The Federation Gets A Bit Darker...
One complaint I often hear from science fiction fans is that Star Trek, in particular Star Trek: The Next Generation, is too utopian and preachy. I've only seen a little bit of TNG (the main Star Trek series I watched was Voyager), but the "we've outgrown our infancy" quote you can find here (I tried to find the video on YouTube and couldn't) is a fairly blatant example.
(Later Star Trek series have moved away from this, one example being the Maquis plotline in Voyager and Deep Space Nine. It's exemplified by the "it's easy to be a saint in paradise" quote from Sisko here. If I may be a bit self-promotional, here's how Star Trek would look if it was me implementing the basic concept...)
Well, here's an alternate-universe fan-fic from the alternate-history forum entitled "Star Trek: Utopia's Fall." It diverges from canon with the failure of Operation Return, the mission to recapture Deep Space Nine from the Dominion. To let you know the tone of the work, I'll leave you with this quote from Quark, which is largely a canonical quote from a DS9 episode:
"Let me tell you something about the Federation. They're wonderful, friendly people, as long as their bellies are full and their holosuites are working. But take away their creature comforts, deprive them of food and sleep, sonic showers, put their lives in jeopardy over an extended period of time and those same friendly, intelligent, wonderful people...will become as nasty and violent as the most bloodthirsty Klingon. You don't believe me? Look at those faces. Look in their eyes."
We're still in the early stages of the story, but the gist of seems to be that the Dominion wreaking more havoc against the Federation in the early days of the war burns away the complacency, laziness, sanctimoniousness, and arrogance of the TNG-era Federation and forges the sword that will ultimately destroy them.
A hint of things to come: The author references Section 31 building Genesis Devices...