There has been a few Star Trek and MLP crossovers. One I think could work for a fan fiction is in the Original Series. All the way back to Kirk! The Episode is "Who Mourns for Adonais?" Season 2 Episode 2 it aired 22 September 1967.

In that episode, the crew of the Enterprise meets an alien claiming to be Apollo. Turns out his race had met humans long ago and inspired the Greek pantheon and myths.

Now I know what the next question is how does this tie into MLP. Well, the Unicorns, Pegasus, and other life on Equestria do have a strong Greek element. My Idea is that what we now know as Equestria or Equus. Was once a colony of these Aliens. Seeded with life from both their homeworld and Earth. That's why it has many earth plants as well as life not from our world.

It would also explain the accent temples Daring Do visits. Including the Fortress of Talacon with the Rings of Destiny could control the sun.

In the Episode, it is mentioned that Apollo has an extra organ that processed energy. The energy that could be magical energy? He does seem to be able to have many magical-like abilities

This is one Star Trek / MLP link a writer could follow. I, however, am not a skilled enough writer to do it justice.

In the comics, durring the Return of Chrysalis arc, they show a map of the area South of Equestria. On that map, one of the landmarks is a bit alien, scifi-looking obelisk which is a dead ringer for the war memorial encountered in Voyager episode called Memorial (Season 6 ep 14).

This would mean that on the ponies' planet there sits a Nakan monument. A device which beams experiences into the heads of anyone nearby via a synaptic relay. The one Voyager encountered was almost our of power, which means the one on the pony's world could be long long long dead. Howeaver it would mean that Equestria is on a planet within the Delta Quadrant close to the galactic core and near the Beta Quadrant border as in that episode Voyager is between 35000 and 30035 LY from Federation space.

6144598
Got a picture of it? It may actually be a reference to the Preserver Obelisk from The Paradise Syndrome.

6144614 Your right, that's actualy what it looks like. My bad! I got the two monuments mixed up. Still, it's more evidence that the setting is in the Trek univerce. Heck, unicorn and pony magic even works there!

6145422
Or at least that the comic team likes making references.
I mean, they've also reference Quantum Leap.

6145611 Yes, but building a fan theory means ignoring the other references