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 Post Nuptials

In the aftermath of the wedding, Spike is bitter and avoiding everyone. Twilight's determined to find out what's bothering her charge, but she walks a very fine line when dealing with an emotionally distraught child.

Meanwhile, Rainbow Dash suspects something's wrong with Scootaloo, so she starts spending more time with her in hopes of picking the secret from her brain. As she begins to truly mentor the young filly for the first time ever, she begins to see the advantages to having a little sister.

And while all this is going on, Pinkie is struggling with some old family issues that have been brought to the surface, meaning she might have to confront her past at last.

Art by Conicer

Tiberium. The infamous green crystal that destroys entire worlds in its wake of global proliferation. It has been a little over a century since the Tiberium threat was first wiped out on Earth, and with it, the primary vestiges of the Brotherhood of Nod. When the GDI advanced humanity to the stars, they found that Earth had not been the only target of the alien Scrin: dozens of other worlds had already been claimed by Tiberium, and the Scrin returned in full force, attacking human colonies across space, stopping human expansion. To fight back, the GDI undergoes a reformation to become the Interstellar Defense Intiative (ISDI) and enacts the Hallman Directive, designed to stop Tiberium spread wherever it may be; such a protocol brings the reincarnated ITC Methuselah to a planet being ravaged by the green crystal, and the forces under Commander Martin Alexandra deploy to stop the threat.

Crossover Material: Command and Conquer - Tiberian Series/MLP
Rated Teen for Graphic Violence and Language

When the Elements of Harmony defeated Discord, they did their job too well, and completely undid all of the things Discord directly did...

... Like send a subcontinent from earth into a pocket dimension so he could focus properly on his toys. And now Equestria has appeared on Earth.

Yet, neither side was completely ignorant of the other. On Earth, there was the show "My Little Pony: Friendship is Magic" and in Equestria there was the ever popular movie serial "The Dark World: Technology is Courage" which was a favorite of colts everywhere as well as the "Pumans".

And now both sides learn through an event that the other is real. Come join us as we watch as both sides learn to work and live together. And as they find out that events on their respective fiction was not as nice as it seemed as we widen the lenses of the view points...

A Round Robin created on SpaceBattles of which I am a participant and am posting with all their permission.

The Mare in the Moon has returned, and the dark power that created Nightmare Moon is awakening again with the aid of a magical Moonstone. The two princesses and the Mane Six must use the Elements of Harmony to banish the darkness once and for all. Meanwhile, on Prehistoric Earth an alien artifact identical to the Moonstone falls into Predacon hands. What does this mean? And what will happen when a rift in space is opened between the two stones, pulling the Transformers into the strange, new world of Equestria?

(Note: It gets dark in places, but there is no explicit violence or gore.)