Shortly after the banishment of Nightmare Moon, an angry Celestia has a troublesome guest for dinner.

"OH! That would be the Elements of Harmony! They're the neatest thing! We each get a jewel necklace--Twilight gets a sparkly tiara--and we used them to defeat Discord and Nightmare Moon with rainbows that go pewpewpew-!"

A clawed glove wrapped over Pinkie Pie's lips, silencing her.

"What does the pink one speak of, pony?" He demanded of Twilight, who sputtered at his question. "Do these 'Elements' hold the power to resurrect humanity?"

"I'm... not sure." She returned, halfheartedly. "They're pretty powerful..."

"Where are they?"

"In Canterlot, the city on the mountains, but-"

He dropped Pinkie and stomped off, leaving her to flop around her stretched-out lips. Twilight saw that he was going out the door and in the direction of the city she had mentioned.

"W-wait! Stop!" She galloped after him.

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

"My handsome little cherub, close your eyes.
Mommy's going to give you clear blue skies.
So you’ll laugh and dance and play in the air.
And sing the song of angels everywhere."

A thousand years after the banishment of Princess Luna to the moon along with all the Imperialists who swore allegiance to her, a complex lunar society has been built beneath the surface of Nightmare Moon's prison. In just a few decades, the despotic Empress of the Lunar Empire will have gained enough power to return to Earth and invade Equestria, transforming it into a dystopian realm of darkness. The only thing that stands in Nightmare Moon's way is the fulfillment of a prophecy, where the stars will aid in her escape so that the Elements of Harmony may exorcise her of her evil before she becomes dangerous enough to overcome her sister, Princess Celestia.

Enter Myrk, the former Captain of the Lunar Night Wraiths. Once the chief bodyguard to Nightmare Moon, he has since been branded an exile and traitor to the Empire. The Imperial Lunar Rune Guard hunt Myrk throughout the subterranean cityscapes of the moon, until he is forced to hide within the sarosian district of Tranquility deep below the outer laters.

Now, after having reunited with his half-sarosian lover, Choral, Myrk must embark upon a dangerous mission to deliver a captured piece of Princess Luna's magical essence to the lunar surface, in order to cast a beacon that will summon the stars and pave the path towards Nightmare Moon's righteous defeat.

This is an indirect prequel that takes place within the same universe as The End of Ponies.

This story is a sequel to Smoothing the Knots

Princesses Celestia and Luna take tea under less than ideal circumstances: house arrest for psychiatric care following Luna's revelation about the her use of the Tantabus to torture herself.

Ever the thoughtful sister, Celestia tries to help Luna open up about her addiction to guilt and suffering in order to understand why Luna isn't happy now that the pain has finally left her. But Luna has a very different topic she wishes to discuss.

When Twilight visits Celestia's private hall of stained-glass windows, each bearing the image of a long-gone friend, one in particular catches her eye.

Who was this pony?

Why was she so important to Celestia?

And why does she look so familiar?

There is now a Spanish translation of this story, courtesy of Spaniard Kiwi

[Complete! With TVTropes apparently!]
Also, apparently, an animated trailer.

In a world of brass and steam, Twilight Sparkle had thought she had made a life-changing discovery with the invention of the telescope. For better or worse, she was correct.

Now her discovery has not only changed her life, but the lives of those she seeks out in her desperate attempt to contact the only other creature as lonely as Twilight herself.

It all would have been much simpler, but it had to be the one Twilight could only call The Mare on the Moon.

Decidedly not within walking distance, then.

[Featured on EQD before story was meant to be submitted. 4/03/2015]

[Editing team: Southpaw, Wolfvenom, Maskedferret, SwanSong and BluePaladin42, without whom this story would be a fraction of its current state.]
[Special thanks to Novel-Idea for the updated cover]

Deep under the resplendent city of Canterlot lies a web of vaults, containing many secrets hidden from the common folk. One of such undercrofts shelters an extraordinary artifact – the crimson horn of King Sombra, the uneasy spirit of the corrupted unicorn still within it.

After months of careful consideration, Princess Celestia ventures down into the delves underneath to confront the fallen king, determined to aid him and bring him serenity at long last.

Mystery. Love. Magic. Murder. Truth. These are all important elements in the murder mystery Fluttershy has written, and is now asking Twilight to read. But the novel stars 'Twilight Sparkle', and she wrestles with the metafictional dissonance involved in reading a novel about herself and her friends. Twilight must do her best to solve the mystery, reconcile her own feelings about this ordeal, and figure out just what Fluttershy is trying to say by writing all of this in the first place as the lines between fiction and reality begin to blur.

This is a thematic crossover with the visual novel 'Umineko No Naku Koro Ni.' No prior knowledge of Umineko should be necessary.
Cover art commission done by SynCalio