Twilight Sparkle has turned evil and is bent on taking over Equestria for herself; she has already killed Applejack, Rarity, Rainbow Dash and Princess Celestia, stealing the Elements of Harmony, using their raw power to destroy anyone who stands against her path to total domination. Pinkie Pie and Flutterhsy evading Twilight's pursuit, with their respective Elements of Harmony in hand, Twilight enlisted Discord to draw out the two remaining elements by turning all of Equestria into a post-apocalyptic wasteland, and when that didn't work she released all foes she had previously defeated, including the likes of Queen Chrysalis, The Dazzlings, and Lord Tirek.

Sunset Shimmer, a former student of Celestia's, now works as a smuggler for anyone with good enough cash, all while avoiding rival employers and Twilight's Royal Guards, dubbed "The Alliance" by her and other smugglers.

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Inspired by works such as: Star Wars, Firefly, and Fallout
Art by bakki

Edit (2/10/18): Revised almost everything, up to chapter 7 and the title.
Edit (5/31/21 - now): edited for better, more consistent terminology, word choice and other cringey things.

A former pink pony finds herself in a new, hostile world and a new friend who's perhaps even more hostile. A small, angry man finds himself with a new friend he didn't want. Can they make it through this new misadventure together, or is it the universe that needs to watch out for them?

Cover art used with permission from Technaro.

For two years I've been hiding, for two years I've tried to just live my life. But it all came crashing down the day I chose to have lunch at a Diner. Now I'm forced to run again, forced to leave the life I tried to build. But what choice do I have, what choice does a mere clone have when she shouldn't exist?

"Sis, I know you always told me that the farm is our home and that we all belong there, but you also told me you had to leave to find that out. I hope you can understand. I'm tired of ponies telling me that I'll find out who I am if I wait. What kind of boring self am I ever going to find by just sitting around doing normal stuff?"

—

Cover image by Icaron, used with permission.

Since the Timberwolf incident, Applejack hasn't been feeling well. She can't eat, she can't sleep and she's not sure why.

Little does she realize that she's suffering from the deadliest disease of all: love.

But who is she pining for?

Melodramatic reading by BigApplePie.

Fan Art by byLisboa

This story is a sequel to Bride of Discord

Discord and Fluttershy are blessed with a daughter named Screwball, who is gifted with incredible power that attracts the attention of the Queen of the Changelings...as well as her son.
When disaster strikes that tears Screwball's family apart, it is up to her to bring it together again.

New cover art by floppy-fluttercord

This story is a sequel to I Love Ya to the Core

Spike finds himself on a game show hosted by Discord where he has to choose between three mysterious bachelorettes, not realizing that this is a ploy to settle a love triangle he has not been aware of. Who will Spike choose?
Hearts might be broken and secrets might be spilled.
This is a "sort of" follow-up to "Bride of Discord." Not really a sequel, but is set in the same universe.

Cover Image by WolfSpirit1292, who also adapted this into a comic!

What if Discord had not been turned to stone by the Mane 6? What if he had escaped?
It is three years later and the Mane 6 have moved on with their lives, all except Fluttershy, who cannot get the draconequus out of her mind. The others are happy in their new and comfortable lives, until their enemy returns and will only relieve Equestria of his havoc in exchange for a bride.

This has been adapted into an audio series.

Also, here's a dramatic reading by Pablo Didonna, and one by 666HellGirl1

Cover Art by Nstone53

French: http://www.deviantart.com/art/Une-Mariee-pour-Discord-La-fuite-440318295
Spanish: https://www.fanfiction.net/s/10203187/1/La-Novia-de-Discord

*Bronyland Pony Awards Nominee 2013

This story is a sequel to Past Sins

Side-story to Past Sins - Slowly, the wounds inflicted by Nightmare Moon's reign heal. Ponyville is being reconstructed, and the last refugees are leaving the castle. Nyx is with Twilight. Celestia and Luna rule Equestria and guide the sun and moon once more. Everything is as it should be.

But some things are never washed away. These are the things that remain to remind us of the past. They remind us of the good times we've had with friends and family. They never let us forget the mistakes we've made. Everyone has them. Twilight has them. Nyx has them.

And, on occasion, when you share your scars, your photos, and your trinkets with another, they just might share theirs in return.

This story is a sequel to Past Sins

Hearth's Warming is a time for friends and family to come together, celebrate harmony, and welcome the new year. Nyx is looking forward to just this as she rides the train to Canterlot with Spike and Twilight. She's going to meet her extended family for the first time and wants nothing more than to make a good impression. Yet, the sheen of the holidays can't hide the trouble caused by meddling grandparents, relentless reporters, and a paranoid uncle.