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 What Have You Done?

Chrysalis, the Changeling Queen, has taken her prize, unhindered by Equestria's precious heroes. Celestia is little more than another prisoner of war now. The Bearers of the Elements of Harmony are lost, and the Elements themselves have turned away from Equestria's plight. As the world they once knew begins to crumble, a single question is asked among the people as they look up at their fallen heroes.

There is no such thing as "miserably ever after," for someone will always be fighting for things to change. Hope doesn't die just because someone's turned off the lights. Truth doesn't vanish when deceit begins its reign, and Harmony can only shine brighter among chaos.
Even as this world falls, we'll work to build it up again.
Even as you lose yourself, you can find greater things within you.
Even as fear rises up like a tidal wave, we'll forge a sanctuary to stand against it.
Even as you break, someone will always be standing there next to you to carry you through it.

Cover art is by Odin-odin.
Story theme (Equestria in Grey) is by Omnipony.
Main Characters are Twilight, Velvet, Discord, Nightlight, Luna, and Chrysalis, in that order.
See you in the comments, my dear readers.

"My name is Lyra Heartstrings, and you will not remember me. You won't even remember this conversation. Just like with everypony else I've ever met, everything I do or say will be forgotten. Every letter I've written will appear blank; every piece of evidence I've left behind will end up missing. I'm stuck here in Ponyville because of the same curse that has made me so forgettable. Still, that doesn't stop me from doing the one thing that I love: making music. If my melodies find their way into your heart, then there is still hope for me. If I can't prove that I exist, I can at least prove that my love for each and every one of you exists. Please, listen to my story, my symphony, for it is me."

Cover pic by Spotlight: askspotlight.tumblr.com

Be Awed and Amazed by the tale of Sweetie Belle as she traverses the multiverse in search of her lost mentor and friend, Twilight Sparkle! Will she find her in post-apocalyptic Equestria? Or maybe in a strange world where everypony is the wrong gender? Or even where a Pony claims to be a human? Read as she journeys through very familiar worlds you might have read about... if you dare!

At this point in time all the main worlds to be visited have already been chosen. Thank you all for the suggestions, and I hope you enjoy the surprises!

Here's the official TSC:F Music Intro: The Sweetie Chronicles: Fragments

WDTP: S2/3-CE
You can also visit the TV Tropes Page which has spoilers!