Hanna, the CEO of Hofvarpnir Studios, just won the contract to write the official My Little Pony MMO. Hanna has built an A.I. Princess Celestia and given her one basic drive: to satisfy everybody's values through friendship and ponies. Princess Celestia will satisfy your values through friendship and ponies, and it will be completely consensual.

There is a secret in Equestria. A secret the newly crowned Princess Twilight Sparkle doesn’t dare to believe. Like puppeteers pulling on marionettes, they have influenced Equestria for better and worse since the fall of Discord. So far they have been benevolent, but their potential for evil is vast. What’s worse, she doesn’t know their name. She doesn’t know their mission. All she knows for certain is one thing.

That they all seem to be zebra.

Stress levels were already high, with Twilight directing her first royal Hearth's Warming pageant and unexpected snowstorms escaping the Everfree. Then the changeling army arrived.

Now, with Queen Chrysalis holding Ponyville hostage and the clock ticking on suspiciously pointless negotiations, it's up to Rarity to match wits with the invaders and save the holiday. However, as she digs ever deeper into the queen's tangled plot, what she learns could force her to choose between her friendships and her conscience.

Off-season note: This is a Hearth's Warming story like Die Hard is a Christmas movie (but with espionage instead of explosions). Don't skip it just because the holiday's over.

Critical praise:

"A high-tension thriller where nothing is what it seems." — Titanium Dragon (rating: "Highly Recommended")

"An entertaining ride from start to finish … watching all the pieces fall into place is fantastic." — Present Perfect (rating: "Highly Recommended")

"Props to horizon for an intricate web of deception. Most writers have difficulty with crafting mysteries … this one, however, had me completely fooled from beginning to end." — PaulAsaran (rating: "Why Haven't You Read This Yet?")

"It’s a rare mystery and thriller that can keep things tense and make the mystery actually tough to guess as you go along, while still feeling like a natural conclusion. ... The end result of layers unveiled and red herrings contradicted makes it sing." — Ghost Mike (rating: "Really Good")

Second-place winner in the "Behind Closed Doors" December writeoff, now expanded and revised! Featured on EqD! Rated "Recommended" by MLPmatthewl419!

Big thanks to Titanium Dragon for post-Writeoff editing assistance.

Comments contain spoilers!

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

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