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At last, the second season of your favorite wind mage's adventures in Equestria is here!

Just as Vaati has fully settled down into his new life in Equestria, the unthinkable happens; Ganon appears and declares his intent to conquer. Now, with the Princesses forced into hiding, the Elements of Harmony scattered all across the land, and races all around Equestria suffering under Ganon's harsh rule, it is now up to Vaati, Twilight, and their friends to join forces with unexpected allies, recover the Elements, and take the fight to Ganon. And all the while, an even greater evil plots from the shadows, enacting a scheme centuries in the making that shall soon encompass two worlds that do not yet know the connection they share...

And as the adventure gets underway, one by one, the Mane Six begin to have nightmares...

Meanwhile, the Cutie Mark Crusaders must combat the darkest depths of madness and twisted illusions if they want to save Scootaloo from falling victim to the evil power that weaves the strings of all their fates...

Rated T for action violence, minor language, mildly suggestive themes, and some scary/disturbing images.

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

Applebloom just wanted to spend a day with her friends, crusading for her cutie mark. Instead, she found something even deeper and more troubling about herself. Turns out she's not even a member of the Apple Family by blood. In fact, she's not even truly native to Equestria! She's an alien! An alien robot no less!

Now Applebloom will have to deal with the reality of her origins and try to cope with them and her newfound abilities as she moves towards her future; a future that just might never come to be if her new foes have anything to say about it. Decepticons are, after all, a monstrous cabal.

Now, it's up to Applebloom to light Equestria's darkest hour.

Cover image credit goes to Inspectornills

Strange nightmares are plaguing the ponies of Equestria.

Somepony must help ponies to face their deepest fears, but unless Princess Luna is able to discover who—or what—is responsible, the nightmares may never end.

Scootaloo is ready to prove that she can be as fearless as her big sister, Rainbow Dash, even if it means never having a peaceful night's sleep again.

Just about everypony in Ponyville knows Scootaloo. She's your normal, carefree pegasus foal who crusades for her cutie mark, zips around town on her scooter, and looks up to her idol Rainbow Dash. But what if that's not all there is to her? Scootaloo worries that her friends will find out that she's not the foal they know and love, or that she's not even a foal at all. But, when her secret does come out, their reactions might surprise her.

Rainbow Dash attends her hometown's Millennial Summer Sun Celebration, where she meets a peculiar pink pony. When a strange portal appears during the testing of Twilight Sparkle's latest invention, and pulls their new companion inside, the two friends give chase and embark on the most important adventure in all of history.

Equestria Daily | TVTropes

The Griffin Kingdom prepares an invasion on Equestria, and when the Wonderbolts are incapacitated by two griffin aces, a group of pegasus ponies, assembled by Firefly, becomes the land's main aerial defense force, supporting each other in the hardest of times. It's a story of revenge, friendship, sadness, struggles and sacrifices, a war which will change the lives of many a pony and griffon...

Pre-read and proof-read by Rethkir