One fine, perfectly normal day, Twilight unlocks the doors to her School of Friendship... and promptly loses consciousness.

When she comes to, she finds that her friends, mentors, other ponies she knows and even a couple unreformed enemies are with her, and her School has been radically modified, relocated and encased within a barrier. A strange little black-and-white bear tells them that they now live here indefinitely; the only way they can leave this place is if they kill a fellow pony and get away with it in a trial.

But Twilight has nothing to worry about. As long as she believes in the Friendship between herself and the others, there has to be a way for everypony to escape alive and well. Surely nopony would even dream about killing another pony... would they?

Moon Dancer has been awarded a prestigious grant to study the Everfree Forest and its history, and so she's moving to Ponyville. In the midst of settling in and making new friends, she meets and becomes completely enchanted by a shy, animal-loving pegasus.

But as these two nervous little weirdos start an adorable, awkward relationship, it becomes clear that not everyone is happy about this turn of events.

Now with a sequel!

...And another sequel!

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 Pandemic

Six months ago, the world humanity knew had been irrevocably shattered in a way they would never have imagined. ETS -- Equine Transformation Syndrome -- had arrived, a powerful transformation spell attached to an otherwise ordinary flu virus. Only with the assistance of Equestria in the form of Twilight Sparkle and Starlight Glimmer had ETS been stopped from transforming all of humanity into ponies.

Humanity had been saved, but at a cost. Hundreds of millions of humans had been fully transformed into ponies, and many did not want to go back. The United States was hit especially hard, with over a quarter of its population as ponies. Friction between humans and ponies, Earth and Equestria, has been growing. Families torn apart by ETS had yet to reconcile.

The collision of worlds that the pandemic had brought had only just begun.

Updates weekly FOR NOW -- may switch to every two weeks in the future. I will announce as such.