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

This story is a sequel to Doctor Whooves: Invasion of Manehattan

Starlight Glimmer has succeeded, she has managed to steal one of the Star Swirl spells from the forbidden section of the Canterlot library and, after months of work studying countless tomes of arcane magic related to time, she will be able to defeat that princess of friendship and her friends before even meeting her.

All she has to do is stop the brat that was Rainbow Dash from doing the Sonic Rainboom on her. But before she does, somepony stops her and asks her a simple question, 'are you sure you want to do that?'

When Fluttershy went to bed, she was a normal mare. When she woke up, she could see numbers floating over everypony's heads. They were timers, each one counting down to some unknown event. Most ponies had timers that wouldn't end for years, some for many decades. But everypony had different numbers.

So why does Rainbow Dash's timer end in three hours?

Editing provided by TheMaskedFerret and SolidFire.
Cover art by HopefulSparks!
Spanish translation by SPANIARD KIWI!

When sorting through a horde of ancient artefacts Fluttershy and Rainbow Dash accidentally activate the magical powers of a pair of bracelets which force the wearers to be in constant physical contact with one another. Stuck together until Twilight manages to find a way to remove the bracelets, the shy and timid pegasus must cope with re-emerging feelings, while the athletic and rash pegasus must cope with the various antics of a bunny rabbit out to get her.

The cover image for this story is the artwork ‘FlutterDash RainbowShy IDK’ by TheDracoJayProduct.

This fanfic features FlutterDash and hints/mentions other pairings such as SpArity, RariPie, and SweetieSpike to a lesser degree.

I do not - nor do I claim to - own any characters or artwork I use in this story unless otherwise stated - they belong to their respective series and owners.

Now with a fan-made TV Tropes page created and maintained by Zyr1987 because readers of this story consider this to be that awesome.

Daring Do cannot believe her luck when she is asked to help explore the most ancient tomb known to ponykind. But terrible danger awaits her, for beneath the earth rests something beyond equine understanding.

Warning: comments contain ending spoilers.

TVTropes page.
Alternate ending by Duplex Fields.
Archived in the Pony Fiction Vault.
Reviews:
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Tempest Shadow finds the path of reformation is not easy for her... it just doesn't feel right. Then she learns of a disquieting trade going on in the Southlands... and then a close friend is ponynapped... and she discovers exactly the kind of pony she is meant to be.

Sequel to MLP: The Movie, covering Tempest's reformation and also tying up loose ends in the movie and prequel comic.

User Spaniard Kiwi was kind enough to post a Spanish translation over on DeviantArt -- check it out!

For more fun with Tempest Shadow, see the Nightmare Night story,
Nightmare Fight.

This story's timeline is also continued into Season 8 by Twilight's Pirate School.

This story is a sequel to Changeling Courtship Rituals

Queen Chrysalis attacked Canterlot, brainwashed Twilight Sparkle's brother, kidnapped her former foalsitter, defeated her mentor in combat, and conquered her kingdom. She kidnapped the sisters of Twilight's friends, turned them against one another, and tried to drain all of Twilight's magic. Queen Chrysalis has, at every opportunity, done her very best to utterly destroy Twilight Sparkle's life.

For some reason, this has not caused the pony to fall in love with her.

However, due to Twilight's misunderstanding of changeling customs, it does mean they are now married. Twilight eventually managed to tell the Queen the truth, but she forgot that whether it's a kingdom or a heart, changelings conquer.

And since the changeling way of conquest didn't work, Chrysalis is determined to try the pony way. The only problem is, of course, she has no idea what that is. But she knows someone who does: Princess Cadance.

Now, with the absolutely sincere help of her mortal enemy, the pony she once locked in the caves beneath Canterlot while trying to steal her husband on their very wedding day, Queen Chrysalis is going to woo the sister-in-law of that very pony.

Surely this is the most perfect plan ever devised.

***

Proofread by ShutterflyYay.

Takes place roughly after season five (so Starlight Glimmer is running around occasionally)

With Twilight Sparkle still adjusting to life as a princess, Rarity becomes convinced she can help her friend by finding her a special somepony. And when that somepony turns out to be Fluttershy, awkward dates and adorable moments are sure to follow!

Cover art by mocha-creme (Thanks to OminousBrony for the suggestion!).

For a different take on the same characters, be sure to check out my RariTwiShy story, Our Lady's Courtship.

For years, Twilight Sparkle and Queen Chrysalis have been at each other's throats. Both have experienced victory over the other, and both have experienced defeat. Out of all the creatures in Equestria, none despise each other the way the pony Princess and changeling Queen do. They seemed destined to remain locked in battle forever, or at least until one is finally dead at the hooves of the other. The cruel insults, the vicious loathing, and the powerful spells that have passed back and forth between them at each meeting have become the stuff of legend.

Imagine Twilight's surprise when she finds out changelings consider this dating.

And now they're married.

***

Sequel: Pony Courtship Rituals

***

Some beautiful fanart of the end of chapter three was done by Dmann892; you can see it here.

More awesome fanart, this time from chapter one.

Now with a TvTropes page (obligatory TvTropes warning goes here).

If you want a Russian translation, you can find it here.

There is now a reading of the story on Youtube, which starts here.