The newly coronated Princess Twilight suffers an abrupt tragedy. Having lost two loved ones, she begins to question her own mortality, and that of her friends.

AJ, Dash, Rarity, Pinkie, Fluttershy. . . they are just the beginning. Twilight will live for thousands of years, so every pony she cares about—every pony she will ever care about, will die.

She could barely handle the pain of one funeral, let alone the thought of hundreds of them. Twilight finds a clever way to ensure all of her friends never die. They can’t all be ageless alicorns, but they can all move into Twilight’s Dollhouse. Then they can be best friends forever.

Sequel: Twilight's Dollhouse 2
Fanmade Song: Twilight's Dollhouse

Source: Dreampaw
Editor: Gage of Grandiloquence, Breath of Plagues
Pre-read & Idea pony: TypeWriterError,
v1.1 Revised chapters 1-10 on May 1st 2013
--Pending a few more revisions, including ch. 14
Now on TV Tropes.

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!

Princess Celestia tires of constantly being surrounded by decorum, deference, and formality, and decides to take a day off from being Princess. But visiting Ponyville incognito is harder than she expects. Will she be able to fit in and make friends without blowing her cover?

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

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

Luna discovers something hidden from Celestia for twenty years, now, with emotions running high, she enlists the help of the Mane 6... but what seemed to be a single mystery, soon reveals a darker and much more complicated plot that will soon decide the fate of Equestria.

Check out the Empty Room TV Tropes Page (Warning: Spoilers!)

Revised chapters edits and proofing (with many thanks) by: lammy, Trevor, Nick Nack, Fifth Alicorn

Canterlot... For centuries, Canterlot was the shining gem of Equestria, the pinnacle of pony society. Now, it’s a reminder, a bleak and monolithic warning to the world. 

Changed by the chemical and technological poisons that plague the mountain, an abomination of nature, I wander the greatest disaster Equestria has ever seen. 

... I will escape eventually, and when I do, I hope my friends still see me as Twilight Sparkle, and not the monster that hides among the ruins. 

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.

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

War comes to Equestria: with despair, with starvation, with suffering and with sacrifice. And the ponies must learn how to keep true to their values while surviving not just the rigors of battle, but the desolation of total war.