A horrible Cataclysm has turned all of Equestria into a Wasteland of barren ash and twilight desolation. The Sun and the Moon have been destroyed. Everypony has died--including Princesses Luna and Celestia. But one pony miraculously survives; she is a lone wanderer, the last of her kind, surrounded by menacing creatures that hate her. She navigates the Wastes in an airship and scavenges off the blighted landscape to keep herself alive.

Then one day she meets an old companion who grants her a gift, the chance to go back in time to the warm and sunny days of Ponyville, where her dead friends live in happiness. How far will the last pony venture into this joyous age of Equestria, even if she fully knows that there is no way to change the horrible fate of everypony she loves?

2013 Edition: Smaller Chapters, Better Grammar, and a Few New Scenes

(A shout-out to Vimbert, pre-reader and gentlecolt)

This story is a sequel to Of Solicitude

Ten years after a massive war, Equestria has changed. The Empire now rules over all, giving peace and prosperity to those that deserve it, but some are against this new rulership.
The CMC, a small, raggedy group of smugglers working for the Apple family, are caught red-hoofed by an Imperial patrol. As the friends fight for their lives, they learn about themselves, each other, and the world they now reside in.
Meanwhile, in Canterlot, Emperor Blueblood has amassed a massive fleet and is preparing to smash what is left of the rebellion under the oppressive hoof of his Empire.

Fantart:

http://www.youtube.com/watch?v=cSqZZHhQa_I

http://www.youtube.com/watch?v=JE7m2dk8FB4&list=UUS5YHp6kB61DHIXt8THr4iQ&index=1&feature=plcp

(please read entire description)
(News: first prelude 'Unreconciled' is being written for release before chapter 3)
After nine relatively peaceful years in Ponyville, Spike falls into hibernation and a protracted nightmare.
Upon awakening, the uncertain future of the World is thrust onto him by a message from the Great Teacher, Starswirl,whom may yet live.

The Royal Sisters are trapped in conflict with a Draconic entity capable of destroying the universe.
All the while, Spike and the Elements of Harmony each must seek out powers and wisdom rooted in the origins of the world.
They do this in hopes of overcoming a foe that roils the black and starry depths of the very heavens.

In their absence, the former CMC and the uprising youth of Ponyville grasp power in the midst of possible griffin invasions from the Avian continent.

[key: Telepathy; Thoughts; EMPHASIS in dialogue ; Magic Spells/Special Abilities ; * marks objects or facts related to side stories]

NARRATIVE BRANCHES
(Chronology of back-stories in the Machi-verse)
<prelude>"The Wyrm Has Turned" [un-posted]
<prelude> An Astronomy of Souls [un-posted]
<prelude>Waiting For Galaxei [un-posted]
<prelude>Too Far From The Tree [un-posted]
<cross>Appleseed Hill [un-posted]
<cross>Gambling in the Dust Trough [un-posted]
<cross>Absolute Defense [un-posted]

[credits]
Cover: dsurion (http://dsurion.deviantart.com/) edited: Muzzledelk
editor/illustrator Credit:
AwSweetHolyHell, Frees,Quisky, Karon, lordlyhour, Samaru163, genocidal brony...
all other contributions are credited within the work.(all art use has been permitted by the respective creators.)

=====Originally Written February 2012===== EQD Post=====
After overwhelming Ponyville's mayor, the main six must fill in as she takes a much needed vacation. Yet, only one pony can take the title of mayor at one time. Which of our favorite ponies will be the first substitute mayor? How long will she be able to last before passing the job to somepony else? And in the end, will Ponyville survive long enough for its real mayor to return?

This story was written as a prize commission for the Smile Album Charity Event. The original prize was one by Stormy Seas and he provided the original premise for this story. He always wanted a story that could be shared and enjoyed by everyone, so be sure to thank him if you know him.

Chrysalis was broken and defeated. Had she not come across a loving mother and child, she would be dead. But she need to feed, and thus an idea struck her.

(This is a tie in with both Resistance: Equestria and Chaotica.)

When Ruby boards the first trans-oceanic flight in Equestrian history, the last place she expects to end up is stranded in the middle of Eternity's Crossing in the wake of a horrific zeppelin crash. After a mysterious tower leads her and a fellow survivor to discover a twisted and fragmented city twenty thousand feet below the surface of the ocean, though, a bit of fire and smoke is the last thing she needs to worry about. Between the horrendously disfigured residents and the paranoia of the madmare who once built and controlled it, daily survival in this corrupted utopia is anything but a guarantee. But with the help of some new friends and a few genetic enhancements, Ruby isn't going down without a fight, and in the process might just discover that the deadliest weapon in Harmony is herself.

An adaptation of BioShock for the world of MLP. Written to be comprehensible to anyone, regardless of whether they've played the original game.

Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.