I know there have been several instances of a civil war occurring within the Federation at various points in the novels and such (most seem to end up with Vulcan leaving for some reason), but what if there was a civil war that was a little more insidious, fought between Section 31 and an element of Starfleet/UFP dedicated to bringing it down?
S31 is meant to be a super secret group that most within the Federation and Starfleet doesn't even know exists, so we have no idea of the number of agents, operatives or informants they have on the books, but they do look to have the fingers in pretty much every pie across Federation space. In the DS9 Relaunch books, Elias Vaughn is part of a "cabal" dedicated to taking them down, again we have no way of knowing how large this group is. So what if both sides ended up facing off against one another, a conflict that spilled out into a full on civil war within the fleet, one that would ultimately bring an end to S31 once and for all.