It has been several months since the disappearance of Twilight Sparkle..

One night, after watching her sister raise the Moon and set the heavens alight, Princess Celestia begins to bed down for the night, only to be interrupted by portal forming in her room. From out of the portal comes none other than Twilight Sparkle, garbed in strange armor.

Princess Celestia, along with Luna, Cadence, and Shining Armor, are overjoyed by the Element of Magic's return, but are justifiably curious as to where she had been and what she had been doing. And so, Twilight begins her tale. A tale of survival against impossible odds. A tale of a people fighting for the most basic right of all sentient beings. The right to exist.

This story is a sequel to Petriculture

It's been several months since Pinkie Pie made a stunning admission about her past that permanently changed her relationship with her friends, particularly Twilight Sparkle, but life seems to have settled back to normal (well, normal by Pinkie Pie's standards, at least). However, when an old nemesis returns and ensnares Twilight in her influence, it's up to Pinkie to make things right.

This is the second story in The Petriculture Cycle. There is a TV Tropes Page for the entire Cycle here.

Cover image by Page Turner; "Princess Twilight" vector by Nianara.

"My name is Lyra Heartstrings, and you will not remember me. You won't even remember this conversation. Just like with everypony else I've ever met, everything I do or say will be forgotten. Every letter I've written will appear blank; every piece of evidence I've left behind will end up missing. I'm stuck here in Ponyville because of the same curse that has made me so forgettable. Still, that doesn't stop me from doing the one thing that I love: making music. If my melodies find their way into your heart, then there is still hope for me. If I can't prove that I exist, I can at least prove that my love for each and every one of you exists. Please, listen to my story, my symphony, for it is me."

Cover pic by Spotlight: askspotlight.tumblr.com

When Ruby boards the first trans-oceanic flight in Equestrian history, the last place she expects to end up is stranded in the middle of Eternity's Crossing in the wake of a horrific zeppelin crash. After a mysterious tower leads her and a fellow survivor to discover a twisted and fragmented city twenty thousand feet below the surface of the ocean, though, a bit of fire and smoke is the last thing she needs to worry about. Between the horrendously disfigured residents and the paranoia of the madmare who once built and controlled it, daily survival in this corrupted utopia is anything but a guarantee. But with the help of some new friends and a few genetic enhancements, Ruby isn't going down without a fight, and in the process might just discover that the deadliest weapon in Harmony is herself.

An adaptation of BioShock for the world of MLP. Written to be comprehensible to anyone, regardless of whether they've played the original game.

Spike only wants things to stay the same. Time, however, has other ideas. He's going to need a lot of help... An everypony story.

(Cover image by Rannva)

Twilight is invited to Canterlot to compete with some of the greatest magicians in the world for the Moonstone Cup, a prestigious award for the most powerful and skillful magicians, unicorn and otherwise. Can she win? What sort of competition will she face?

Awesome cover image was taken from NoOneBahtim

The wheels of fate turn in mysterious ways. When a unicorn colt has an accident on the edge of the Everfree, nopony knows who he is. Assuming his brain was jostled by the accident, they ignore his absurdist notions of not being from this world, and not being a pony at all. However, when he is involved a terrible incident that threatens the lives of his only friends in the world—Ponyville's three most rambunctious fillies—their friends and family begin to pay more credence to his claims.

For Warren Ashland, the clock is ticking as a chain of events that was set into motion the moment he woke in Equestria comes to a vicious head. The time will come when he must decide whether he wishes to stand alone as a human in the Equestrian world, or give it all up for his newfound friends. His actions will shape the lives of those around him.

Cover art by - GMEiden

Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

This story is a sequel to Aitran

Twilight and Rainbow are asked by Star Swirl the Bearded to take on the challenge of finding his lost wife and daughter in the decaying world of Sohndar, which is ruled by an old enemy of Star Swirl's family who has been trapped there for uncounted years. Although their adventures in the worlds of Aitran have given our heroes the confidence to succeed, they'll soon find that Sohndar is an entirely different bale of hay.

Image by Muffinsforever

Perhaps Doctor Whooves is not a medical doctor or a time lord, but a doctor of psychology.

The following are his journals after he receives instructions from Princess Celestia to permanently set up shop in Ponyville to keep an eye on Twilight Sparkle and her friends, where he learns more than he bargained for.

View the Google Docs table of contents: https://docs.google.com/document/d/1gCeHce9BTZ48P5fxNQDHq7diYlNqJIbkZNdMGLN3H5k/edit?pli=1