Why is Fluttershy so shy? Some ponies are just born shy. Some gain it. But what if Fluttershy isn�¢ï¿½ï¿½t really shy? What if she�¢ï¿½ï¿½s shy to protect herself, because she�¢ï¿½ï¿½s never sure if somepony is helping him? The only way to protect herself is to stay away from others. But she failed to do that, and is an Element of Harmony. But even the Elements of Harmony can't stop him. And now, she has to leave Ponyville before her friends get hurt...
But it's already too late...

(SLENDERMANE) I am disappointed in myself for writing this...

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.)

Daring Do cannot believe her luck when she is asked to help explore the most ancient tomb known to ponykind. But terrible danger awaits her, for beneath the earth rests something beyond equine understanding.

Warning: comments contain ending spoilers.

TVTropes page.
Alternate ending by Duplex Fields.
Archived in the Pony Fiction Vault.
Reviews:
One Man's Pony Ramblings
Louder Yay
PresentPerfect
The Royal Guard
Cleverpun's Critique Corner
The Goodfic Bin

After GLaDOS is uploaded into a potato battery, Wheatley humiliates the AI even further by uploading her into a project that was abandoned by Aperture a long time ago. In the blink of an eye, she finds herself in a deformed body of flesh and bone that resembles an equine, and is just as powerless as one too. It comes with all of its needs and bodily functions as well. To make matters worse, she's trapped in a land full of insufferable creatures that just want to make 'friends.' Will GLaDOS' cold, sadistic sense of humor and morals get the better of the ponies? Or will they peel away the once artificial being's metallic shell and find that there's a softer side? Probably not, but it's worth a try.

Story Theme: Tyler Bates - I Love You (Watchmen OST)

Thanks to Meeester, MrJoshy, and funkyferret for proofreading/reviewing.

Cover by Fedte16.

Mood Wings - Observations on Pegasus Body Language.

When Twilight Sparkle finds this book, she discovers an entirely new field of research. The secrets of pegasus wings lie before her, and she insists on making her own observations on the matter.

How?

Field research, of course.

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.

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.

A Cutie Mark is meant to represent the personality and special talent of each pony that has one. Cheerilee's flowers symbolize her desire to help her students bloom, and the smiles represent the cheer that she hopes to bring to their lives.

At least...that's what she tells everypony who asks.

[SEMI-SAD]

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

A mysterious brown Earth pony with an hour glass Cutie Mark sneaks into Canterlot Castle, only to be caught by Princess Celestia herself. Curiously, Celestia is intrigued by the seemingly endless stream of nonsense this pony is wont to speak. Luna soon joins them, and the group heads into the very depths of the castle, where something has been lurking for far too long...

Author's Note: The story begins with Season 1 Luna, weakened and with very little magical power, as well as having 'flat' hair.

Doctor Whooves is also an Earth pony in this fanfic, as he has appeared as both a Pegasus and Earth pony in show.

Co-Authors: Bramble Rose, MudBug, Diomedes