This story is a sequel to Siren Song

Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Since arriving in Vision, Siren has done things she never thought she was capable of—all in the name of survival. But now she abandons safety to gallop back into the darkness. Determined to do the right thing in a city gone mad, Siren must face the horrors she once fled from. But all is not as it seems in the vast and dark ocean, and Siren’s greatest foe may yet lie within herself.

Book 2 of the Vision series. Sequel to Book 1: Siren Song.

Now with a TV Tropes page!

Princess Twilight Sparkle discovers a centuries-old mystery hidden in the Royal Archives. Her investigation leads through layer after layer of deception and misdirection, setting her hooves on a path that seems to be leading to a mysterious secret. Along the way, she learns that some friendships can be very, very strange.

Book 1 of the Alicorn Adventure series.

AUDIOBOOK by VisualPony
Featured at the Royal Canterlot Library
TV Tropes Page (Courtesy of Sandtalon)
Goodreads Page (Courtesy of Facedeer)
Equestria Daily Page

WARNING: Major spoilers in the comments. Takes place several months after the end of season four. (Not a Da Vinci Code crossover, BTW!)

Do you see a dark tag? No, you don't. Not dark. Well, okay, there are a couple of dark-ish bits, but that's all. Not enough to warrant a tag. Speaking of tags, there really ought to be "Badass Twilight" and "Friendshipping" ones.

Sequels and side-stories (and more) can be found here Offprint and AO3, and a hardbound two-volume set of all that can be ordered from The Ministry of Image.

My editor for the first edition of this story was Gogito, and I can't thank him enough for all the hard work he did. My editor for the revised version was PresentPerfect, and he did a terrific job of getting the story into excellent shape.

This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey

Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Beautiful, gifted, and faithful student of the Princess of the Sun, Siren Song has very nearly everything a pony could want. Sometimes though, in the twilight hours, Siren can see the sadness in her mentor's eyes. Once, ponies whisper, the Princess had another student named Twilight Sparkle, but she left Equestria, never to return. The pony who has a perfect life just needs one more thing—to convince Twilight Sparkle to come home so the Princess will smile again. But when Siren arrives in pursuit of Twilight, she soon finds herself trapped in a city of horrors, with only its monstrous denizens for help.

Now with a TV Tropes page!

A short trip to Canterlot with Rainbow Dash and Applejack is the perfect opportunity for Twilight to test out her new long-distance Teleportation spell. But a nasty cold dashes the hopes of a quick trip, and makes the spell disappear in smoke: instead of arriving in Canterlot, the three find themselves in the nearby Everfree Forest, and discover that their location is not the only thing that went wrong.

While Rainbow has exchanged her wings and tail for a straw blond tail, Applejack has acquired a rainbow tail as well as a pair of strong, blue wings.

While Twilight attempts to find a spell to return the body parts to their rightful owners, the others must attempt to deal with this situation... and with their changing feelings.

After the changelings' failed invasion of Canterlot, Twilight tries to soothe some of Ponyville's rampant paranoia by casting a spell to prove there are no imposters hiding in the town. But her spell leaves her in an alien body, facing a mob of angry ponies who just don't believe her when she says she is Twilight Sparkle.

Or, at least, she was Twilight Sparkle, anyway...

Featured on Equestria Daily, 2/17/13
Cover art is by the awesome and amazing Conicer

Rarity's exploits in "Sweet and Elite" set in motion a chain of events that will find the unicorn dressmaker taking part in the greatest airship race in the world, the Alicorn's Cup. Excitement will give way to terror, as Rarity soon finds herself the victim of a plot against Equestria, and shipwrecked far from home with her least favorite stallion, the boorish Prince Blueblood. Rarity will learn of treachery in Canterlot and abroad, and will have search for something of substance beneath the prince's obnoxious veneer as she struggles to not only save herself, but her entire nation.

Part One of Three
The Adamant Triskelion - Book One: The Flight of the Alicorn
The Adamant Triskelion - Book Two: The Abyssal Forge
The Adamant Triskelion - Book Three: ???

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page