Magic is bleeding out of Equestria and into another realm, a realm where magic does not exist. Twilight must stop the flow of magic before disaster strikes. Can the natives of this realm be of help? How do sapient beings function without magic anyway? What's this about a cartoon?

Takes place shortly after season four.

Two thousand years after the return of Princess Luna, Equestria's technology and magic has advanced far enough that the once far off dream of faster than light travel is now a reality.

And that reality is the ES Harmony, the pride of its designer, Princess Twilight Sparkle, and Equestria's first FTL capable starship. It is due to make its maiden voyage to travel further than anypony before it.

And yet when they receive a distress call from origins unknown, this ship's maiden voyage will become one the crew will never forget.

(Featured on 31/7/2016)
(Not a strict crossover with Star Trek, but here Equestria Girls takes place in the Star Trek Universe)

This is a fic based on the Time Loop Files, the format of which was first codified by Innortal on fanfiction.net.
Here's a brief guide.
The basic idea is, one character (the Anchor, usually the main character of a fictional setting) is looping back to the very first moments of their parent series every time either they die or some kind of time limit expires. They of course end up monumentally stir crazy given enough time.
Eventually others start to loop as well.
The reset is not always perfect. Sometimes a loop's history will be different to the "prime" loop, or canonical plot.
"Crossover" or "Fusion" loops also occur, randomly. These can involve the home loopers having a guest, or the anchor for one universe spending time in another, or replacements of one character by another.
Vacation Loops are where the Anchor (or others) decide/s "buck it" and lets off steam by doing whatever comes to mind. There's little or no attempt to maintain the original timeline.

In addition, and particularly more recently, it should be known that this story has a collaborative element to it - people may submit loop ideas or loops, ideally at the Spacebattles thread (a link to the current version of which is on the Trope page), and they may become included.

There's two page image options, thanks to Filraen - the current page image has been edited by the original creator from this work of theirs.. The other one is here:
http://hourglass-vectors.deviantart.com/art/MLP-Loops-466030169

[First Person] [Alternating Perspectives] [Equisverse Era 1]

In the year 2199, artificial intelligence has advanced to the point where it is no longer practical to have human pilots. This puts Lyra Heartstrings into a forced retirement. Or rather, it puts Lyra from Earth number 7 into retirement. A Lyra born in the extremely distant past before Equestria as human. Lyra 7, an anomaly of the multiverse.

This Lyra is given the chance to pursue the life of adventure she always wanted when her ‘forced retirement moping’ is interrupted by the arrival of an experimental piece of technoarcana capable of opening portals into other dimensions. Unfortunately for Lyra 7, it’s broken, and her tinkering can’t totally fix it. Unable to set her own destination, or fully charge the device and thus unable make more than one portal per charge. Lyra can only wander from universe to random universe in search of the pony (and the proper version of that pony) who made the Vortex Manipulator in order to find her way back home.

Featured on Monday, April 25th, 2016 at 07:06:21 AM UTC.
And also on Friday, July 22nd, 2016 at 09:02:52 AM UTC.
And also on Sunday, August 28, 2016, 2016 at 07:37:21 AM UTC.

For my fan’s convenience: This story takes place in multiple incarnations of the Equisverse. Keeping track of what is and is not cannon to it is futile. All of my stories are canon to this, as this story happens ‘episodically’ in multiple Equestrias. It’s a dimension hopping story. However, this is being done in the more serious tone of Beta, the more “serious” timeline.