This story is a sequel to Second Princess of the Night

With Twilight and Ruby Sparkle settling into their new positions as rulers, they oversee the transition of the bat ponies to their new home. But now that two of the Four Shepherds have appeared, Equestria must prepare itself for the rest. The next Shepherd will be unlike Sombra or Night Walker, as he threatens not only Equestria, but the kingdoms of the other races as well. Awakening from his mysterious slumber, he will carve his way across the land, intent on regathering his unwilling army. But before he manages to travel to the edges of the world, he will leave a parting gift in his wake to Rainbow Dash and four other ponies he chanced upon. With her life forever changed, Rainbow Dash prepares herself for her new fate, as well as finding her place among the ponies that share her future.

Wastelands. Dystopias. Playgrounds for megalomaniacal villains. Each time Starlight forced her into a new world, it was just another variation of Tartarus that she was glad to leave behind and forget about. Unfortunately, thanks to over thirty timeline jumps, Starswirl's spell has gotten worn and frayed, forcing her to stop in this latest world to repair it. Fortunately, things seem relatively peaceful. Unfortunately, Twilight soon finds out the reason for that peace is...complicated.

Princess Celestia: Goddess of the Sun, ruler of Equestria, beloved Princess of ponies. She is loved by all, and loves all in return. A calm and wise ruler, she sits on the throne in Canterlot, maintaining peace and harmony throughout the land.

What most don't know is that her past is much darker: She was once a commander of legions, a warrior and scientist of unmatched skill. Thousands of monsters and abominations fell to her forces, slain in the name of an old leader, one entombed within his own throne. Free of her old form, free of the powers of Chaos, she was cast into a new realm, in a new form, with a new lease on life.

She is the God Emperor, Eternal Ruler of Equestria and Lord of the Imperium of Man.

Has a TvTropes Page. Please contribute.

Comments contain spoilers. YOU HAVE BEEN WARNED!!!

This story is a sequel to The Eternal Lonely Day

On May 23, 2015, the world ended. It wasn't violent, it wasn't bloody, and it wasn't even very dramatic. The entire population of the planet vanished. But they didn't stay gone; almost at once refugees started trickling back. Unfortunately for them, they didn't come back with their humanity intact.

Instead of a single species, the earth is now populated with Ponies, griffons, dragons, minotaurs, and even stranger creatures. What will the remnants of humanity make with their world? Will they remember human achievements, or slip back into primitive ignorance? Learn from our mistakes, or repeat them over and over?

People haven't really changed, only their bodies have. The world now comes with new threats, supernatural as well as mundane. Demons lurk beneath the sea, while strange spirits whisper promises in dreams. Empires rise, dictators control, and ponies have nowhere to turn for help. Nowhere except themselves, and old-fashioned hard work.

This story is effectively an anthology of episodes, each of which will focus on a different time period and different perspective characters.

Latest in the Last Pony on Earth series. If you haven't read that story, start there. This one won't really make much sense otherwise.

Editing provided by Two Bit and Sparktail. Art by the fantastic Zutcha.

April, YOH 1505 (almost 5 years after Luna's Return): Twilight Sparkle and her Companions defeated Starlight Glimmer at Our Town, and return to Ponyville. But though they are victorious, they bear battle-scars on their souls -- and they know that the mad mage is still out there, doubtless lusting for revenge. Sometimes, mere victory is not enough.

Takes place between S501-02 The Cutie Map and S5E03 "Castle, Sweet Castle."

This story is a sequel to Days of Wasp and Spider

Believed dead by their creators, the ponies that will become Celestia and Luna have broken their mental conditioning and escaped into the wilderness. Here they plan the revolution that will free all ponykind, knowing that it is only a matter of time before their ruse is discovered.

Back in their underground arcologies, the ponies' erstwhile masters deal with the consequences of the escape, all the while unaware that something lurking at the bottom of space-time wants them all dead.

A Soot-Covered World, book 2.
Canon species only/no humans.
This story has nothing to do with the Holocaust.
Art by InLucidReverie, used with permission.

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.

Discord, for a master of chaos, was actually a very good planner. Despite the confidence that he would bring Equestria to its knees in mayhem, several millennia of experience had taught him to have a back-up, no matter what. And after watching from the sidelines as Princess Luna became Nightmare Moon, he knew he had found an ace in the hole. Despite his defeat, Discord's greatest trick was still to come.

You know what this means: Equestria's greatest Nightmare is back. And this time, she's not alone.

Edit: Featured 9-27-2013, first time I've had a featured story. Thanks to everyone who's stuck by this story in spite of admittedly slow updates!

This story is a sequel to The Chaotic Touch of Harmony

It has been nearly a year since ponies and Mions appeared on Earth with humanity being divided in how to deal with both. While the ponies in the newly formed town of Trinity work to establish themselves, the rest are scattered throughout the planet while trying to find their place in the world and the Cult of the Koridost is quietly ramping up their genocidal campaign against humanity.

Will Discord’s vision of humanity’s ruin come to pass? Or will his less than direct intervention allow the planet to see a brighter tomorrow?

It is highly recommended to read the first arc because this is a direct sequel and many plot elements may be confusing without previously established context.

Again, thanks go out to Quite Quiet for his editing work.

Excellent cover art by Tulip

Nightmare Moon spends a thousand years banished to the Moon, fighting herself and the Shadows both within and without. She watches civilization rise and spread, a quarter-million miles away.

Can she reclaim her power? Can she overcome the six champions her sister has sent to defeat her?

Why do three of the champions look terribly familiar to the renegade Moon Princess? Why does the sight of one, in particular, break her heart?

And why, as the battle continues, does she increasingly hope that she does not win?

This is an expanded version of the two-part Series Opener. From Nightmare Moon's point of view.

Now with its own TVTropes page!

If you want to find out what the Great and Powerful Trixie was doing in Manehattan, and what happened in some other parts of Equestria during the Longest Night, read An Extended Performance. The direct sequel, however, is All the Way Back.