This may be the strangest crossover idea I've ever had
"Flyer, Farmer, Seamstress, Spy" - a My Little Pony: Friendship Is Magic futurefic in the Stale Beer (flat punch?) espionage genre. Everyone's several years older, and working in some capacity for the Equestria Secret Service. Celestia suspects that security has been compromised and asks Twilight Sparkle to play Whack-A-Mole. Unfortunately, unlike in the good old days, Twilight can't call in her friends to help, as they make up a decent percentage of the suspects. This could end in two ways - either the double agent is one of the Mane Cast, and it all ends in tears; or Twilight's nakama are all in the clear, they team up, and it turns into more of a conventional adventure story as they reforge their bonds of friendship while finding out what's really going on. And then there's cake and hugs. The second option also offers a chance to bring some Trollestia in. (As in, Twilight would have been saved several chapters of unpleasant suspense if Celestia had just *told* her that Rarity was using Spike to fax false information to the pony-Commies. But, no, that's classified information, lol.)