Having binged on MLP: FiM, I want to propose two sort of dark story arcs based on that world. Any suggestions and comments welcome.
I just found a My Little Pony: Friendship is Magic fic called Dark Skies. It's about a group (Shadowbolts) led by a disgraced member of the Wonderbolts aerobatic team and a dishonorably discharged member of Celestia's Pegasi guards who plot to kill the Wonderbolts.
I can imagine this being twisted by Chong in his insane attempts to gain power (hire/bribe/coerce the Shadowbolts to kill Nick or help him gain his powers back.) Or he does a trade (They help him gain his powers/kill Nick, Chong helps them kill the Wonderbolts).
Or borrow a few pieces from another MLP: FiM fan fic (Guardians) and have Chong hire/bribe/coerce some of the Diamond Dogs do his dirty work.
The trigger for both these arcs is that one of the starships is severely damaged (space battle or whatever) and forced to land on the "Pony Planet" and stay until they can repair the ship. Unfortunately, they come under attack by Chong and his hired muscle. Either way, they will still get to live in Equestria for a while and interact with the locals.
Finally, if we can get the soldier ponies (from the fan fic Guardians and they are equipped with guns and explosives) to work right (help in protecting the downed starship, perhaps?), could we include them?
And I guess our characters could end up having to help guard the Wonderbolts if the first arc is used.
If those arcs don't work, an arc where the characters voluntarily land and interact with the MLP: FiM characters in a light and fluffy, nonaction arc could work.