Awake and alone, Applejack will find a way to survive.

And here's a TV Tropes page, if you're into that kind of thing.

After the Changeling invasion, Celestia and Luna make the decision to have Twilight investigate the Elements of Harmony and solve the mystery of their power.

A thousand years later, Rainbow Dash awakens in a world she does not recognize. She has no idea how or why she came to be there. She does not know the language, the geography or any of the rules of this new time. She soon finds allies in Star Fall, a scholarly pegasus whose Talent is Magic, and Astrid, Star Fall's Griffin guardian. Together they set out to discover why Dash has been sent to the future, and how she might return to when she belongs.

War threatens the nations, a Nightmare stalks the shadows, and Rainbow Dash's arrival has turned her into a wild card in a deadly game that pits the law on both sides of a broken Equestria against a mysterious criminal figure, Max Cash. Yet the stakes are higher than anyone knows, for in her research Twilight Sparkle discovered a dark secret about the Elements, something that will shake the foundations of the world.

Cover image by SierraEx
Has a TvTropes page

Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

This story is a sequel to The Sisters Doo

Twilight Sparkle is a scientific pony. She understands things when they are explained.

Pinkie Pie is... uh... not a scientific pony. And she can't explain anything.

But there are secrets in the Wabe that Twilight needs to know, and only Pinkie has the answers.

A side-story to "The Sisters Doo".

It has been ten years since the defeat of the Changling Queen, and Equestria is again at peace. Twilight Sparkle and the Elements of Harmony have reached their prime, and have begun to settle down. Love and life abound in Ponyville, especially for Twilight's friends, but she has nopony to call her own.

There is a reason.

A series of events lead to a horrible revelation, and Twilight is thrust deep into a terrifying web of secrets and lies. Her peace is over.

This time, however, she won't be fighting monsters or madponies. What she faces will be much, much worse.

Act One of Two.

Act Two is here.

Currently undergoing editing by the wonderful Mstar!

This story is a sequel to Lines and Webs

For four long years, Celestia's apprentice Twilight Sparkle, once a model pony and a hero among heroes, has waged a bitter and secret struggle with her onetime mentor. Though she works from the shadows, directing her forces from the Old Capitol in the Everfree Forest, Twilight Sparkle is unable to gain any advantage,

Likewise, Princess Celestia finds her once-faithful student far more cunning and elusive than she had anticipated, and even now searches for a way to bring Twilight Sparkle's rebellion to its knees.

It is a game of greys, of knives in the dark and of poisoned wine, where pawns are moved and traded and exchanged for greater advantage, all the while drawing both sides nearer to the conflict which shall tear Equestria in two.

At the center of this conflict is a new pawn, one who only wished to see the truth for herself. Drawn into a deadly game whose rules she does not understand, Sweetie Belle must learn to survive in a world where all is darkened, and nopony can be completely trusted.

Because when gods play chess, all pieces are expendable.

A nation will crumble, old enemies shall return in the most unexpected ways, and regardless of who is victorious, only one thing can be certain.

Nothing shall ever be the same.

Followed by Stormsinger.

Twilight Sparkle has hit a wall in her studies. So when she is tasked by Princess Celestia with joining an expedition on a faraway island, she can't help but see it as a form of punishment. Nevertheless, she packs her bags and heads to Baltimare, one of Equestria's many port cities. It should have been simple: find a ship offering passage and pay them to take her to Haven. She soon learns, though, that ponies are afraid of the unknown waters past Eternity's Crossing. Despite her best efforts, she is unable to find a ship willing to take her there. That is, until she meets Captain Rainbow Dash.

Brash and enigmatic, Rainbow Dash, along with her crew, are the only ones willing to ferry Twilight on the waters of the Forgotten Sea. She expects six months of quiet travel that will allow her to continue her studies. What she gets is an adventure which makes her realize that, when sailing the high seas, the line between right and wrong is never as clear as it seems.

(Featured on EQD as of 4/28/13
A huge thanks to Breath of Plagues and Amacita, who are amazing editors.
Credit is also due to psychicscubadiver and Zeta040 for pre-reading.)

Daring Do seeks a favor from her sister in Ponyville. Due to buried grudges, things quickly get out of hoof. She soon finds herself on her most perilous mission yet... with her biggest fan in the world. In the midst of truth and lies, loyalty and treachery, love and hate, one thing is clear ― some family situations are stranger than fiction.

The story extends in Through the Looking-glass and What Pinkie Found There and The Daughter Doo: Honorary Cutie Mark Crusader.

Many thanks to Honey Mead and statoose for their watchful and helpful pre-reading.

Ckat_Myla and statoose (CatNStat) have started an excellent reading of TSD.

Giant mutant spiders have ensnared Rainbow Dash's friends with plans to lay eggs in the mares' soft, squishy, bellies. This is the sort of evil that no normal pony can handle. Who should Ponyville call? Who else?

Enter Amethyst Star: Spider Slayer

Dedicated to RazgrizS57 and written in under six hours before a live audience on Google Drive.

Cover art by Darkflame

Now Featured on Equestria Daily!
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Audio version
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Three Nights in Manehattan, a sequel
Hardcover Print-on-Demand Order Page

As a child, Daphne knew of a world where magic lived, where an immortal princess reigned over a beautiful kingdom, and longed to journey there beside Leit Motif, the filly she'd grown to love in the woods behind her home. But one day, when she needed her most, Leit Motif was gone, and she never came back to show her the way. As she grew, she put aside her childish dreams, and taught herself to believe the lie.
When forces beyond her knowing take her sister Amelia, though, she discovers that her childhood fancies were entirely too real, and is thrust into a journey that will take her back to that land she longed for, back to the childhood friend she'd abandoned, and to worlds she'd only dreamed of.

Interview with Pre-Reader Amacita
PresentPerfect's Review