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.

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Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.

This story is a sequel to It's a Dangerous Business, Going Out Your Door

EDIT: 6,000 unique views! Thank you so much to everyone who has read and enjoyed this story.

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An ancient evil has awakened. No, really, it has. From the depths of time, a black, noxious threat has risen up after millennia of imprisonment. It washes like oil over Equestria, swallowing up towns and uncovering terrible secrets long buried. Twilight Sparkle, Applejack, Rainbow Dash, Pinkie Pie, Fluttershy and Rarity are prepared to combat this great darkness. However, to do so, they must uncover the truths about the Elements of Harmony, and the truths about the ancient forerunners of Equestrian culture. What they find will challenge their conceptions of their own places in history and ponydom's place in the world. The six Bearers of the Elements must draw upon their friendship and the strength of their hearts to stand firm against the darkness. If they fail, it will mean the end of everything.

Twilight Sparkle, Apprentice to the Crown, has everything under control. With a sphere of knowledge ever-expanding and a range of powers ever-widening, her world seems smaller and smaller with every passing day. That is, until the day a terrifying vision of the future leaves her convinced that someday very soon, she will take the life of a dearest friend.

Rainbow Dash, the newest recruit of the Wonderbolts, lives in a world without limits. Made of blistering speed and unfettered nerve, she blows past every obstacle that dares to stand in her way. However, when the flight team's training regimen pushes her too far, Rainbow does something she never wanted to find herself capable of.

The Elements of Magic and Loyalty reunite in Ponyville. One must know the answers while the other just wants to run away, but both are on a collision course with a renegade mage desperate to save her imperiled sister, caring little for the consequences of her actions. As the Harmony Storm descends on unsuspecting Ponyville, the fabric that binds Equestria together comes undone, forcing the Elements of Harmony into a race against time if they hope to save themselves, their loved ones, and even the town they hold so dear.

Can Twilight discover the truth behind the Storm before her tragic destiny comes to pass? Will Rainbow surrender to reckless anger if it means the salvation of the innocent? Eyes in the shadows look on all the while, hoping to see the outcome of events set in motion 1500 years ago . . .

From the author of Lost Legacies comes a feature-length prequel made for newcomers and veterans alike.

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.

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.

I am not Twilight Sparkle.

I have her body, I have her memories, I have her power. I am not her, and I have done such terrible things. This is my story.

Once upon a time, Spike went for a walk.

While on his walk, he was judged by an ancient alicorn, lodged with griffons, parlayed with air pirates, charmed a maiden of a mystical race, and dealt with the scourges of hate, fear, and racism while deliberately drawing the armies of myriad nations to the brink of global war.

Once upon a time, Spike went for a walk, and did all of this so that he could keep a promise to the one that meant the most to him... Twilight Sparkle.

In the first of three books, Pillars of the Sun (Chapters 1-15), Spike is devastated by Twilight's fate and grows more and more despondent as he attempts to understand what has happened to his dearest friend. A gentle nudge from a pony he trusts sends him looking for answers. When that nudge becomes a push he unravels ancient secrets... and risks losing himself before his attempt to rescue Twilight can even begin.

[EQD Featured - 10/04/12] Derpy Hooves loses her job and home to personal failures and finds that her life of passivity and reckless indulgence have left her with nothing but an empty void in her heart. When she cries out for help, she receives two answers—one from a concerned Twilight Sparkle who tries to set her life back on track, and the other from a phantom mare who lashes her spirit to that of Silver Cross, traveling warrior and refugee of a destroyed nation.

The clumsy but well-intentioned optimism of the Elements of Harmony and the unshakable death wish of her new "soulmate" are challenging enough, but Derpy will have to contend with overzealous agents of the crown, romantic entanglements, wielders of impossible magic, an outrageously evil despot, and even the dreaded contents of Spike's Secret Stash before all's said and done. Little does Derpy understand that her pursuit of a way to fill the holes in her heart and mind will only draw her ever closer to the forbidden truths of Equestria's Lost History . . .

Cover Art by the talented McLarenF1LM22

The following is supplemental material. Do not read before finishing Episode 03.

APPENDIX

Character Ages
Ponies keep track of their age by seasons, not years. Birthdays are still celebrated annually, but measuring age in years is an unreasonable choice for creatures with a lifespan of roughly 25-30 - there just isn't enough room for demarcations that any reader could relate to. For clarity, the character's ages as of the time of this story are given in three categories below.

MLPL2 Character Age Chart [GDocs Format]

For reference, please note that MLPL2 begins about three years after the Nightmare Moon incident.
More characters will be added as they receive significant roles in the story.

Deleted Scenes

Episode 01, Scene 1 (Draft 4)
Episode 01 [ver. 1]

Cloud Kicker might just have the wildest life of any pony in Equestria. Marvel at the insanity that is her life, and laugh at the suffering of her poor beleaguered best friend, Blossomforth. And maybe, just maybe, there's more to her than just the lovable sex maniac everypony thinks she is.

This is a semi-sequel to "The Incredibly Dense Mind of Rainbow Dash." Not really a proper sequel, since it's focused on Cloud Kicker and Blossomforth instead of Rainbow and Pinkie, but it's in the same continuity. So I guess that makes it a follow-up-side-quel story. Or something. You don't need to have read "The Incredibly Dense Mind of Rainbow Dash" to read or enjoy this, but you ought to read it anyway, just because.

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The central story of the Winningverse.

We got a tag for Cloud Kicker, but Blossomforth still deserves one too.