TD, the human first seen in No, I am NOT a Brony, GET ME OUTTA EQUESTRIA!!! has been in Equestria for a little over a year now and he's just beginning to fully adjust to his life there. However, when he wakes up one morning to discover that five of the Mane Six have switched cutie marks, he endures a significant change when he helps them out.

He is less than pleased.

Edited wonderfully by Strike89

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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.

"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

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.

The "what-if" sequel has arrived -- Equinophobia: Silvery Lies.

"Equinophobia is a psychological fear of horses"
Sometimes you're lucky, and sometimes you're unlucky. Ryan finds herself the latter as she ends up in a world of sunshine, rainbows, and pure horror.

A story of an out-of-place person learning to adapt to their new environment.

Alternate Universe tag for lack of or changes in Equestria Girls elements and the Crystal Empire's history.

Written as the A-side to A Chromatic Scale. The stories are not related otherwise and can be read separately.

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

Jessica finds herself flung into a world she has little concept of. Everything is strange and new to her, but worst of all she cannot communicate with the native inhabitants. A world of monsters and sapient ponies, griffons and other assorted beasts is no place for a human girl.

How will Jessica cope? Without an understanding of their language how will she make her way in the world, will she even be able to ever communicate with them? Why was she even brought into the world and is there even a way for her to get home?

(Thanks to Tulip for the Cover image!)

(Also now apparently has a Tv Tropes page in the making. )

Now has a re-telling in progress focusing on the Equestrians' side of things, A Stranger Among the Voices

Looks like I need to rework large chunks of this story :>
Added tags: Sad
(The sequel is here)
Youtube reads by Spore Harvest start here.

Sometimes, your inventions can bring about great good for humanity. And sometimes, they do the opposite. However, a single man actually did BOTH with his creations, and is one of the few survivors left on Earth after the "Ash fall". He decides, with his breakthrough in spatial rendering, to leave the destroyed Earth behind and go for a new world. He aims to go to a fresh Earth, where everything is as it should be, without his existence.

Unfortunately, he goes slightly off-course, and ends up in the wrong world. How will his technology get him through this?

If any of you don't like a little pseudo steam-punk, then you shouldn't read this, because the main character's technology is heavily influenced on its style...except for three certain things.

The beginning of the story was inspired by "Techno-Babble in Equestria" made by N64Fan. You should go check it out. It's pretty good.

That work of art is "Steampunk Wanderer" by amlaidgh. I only found the name of the artist, so I don't know where it could have been originally posted. The original version of this art seems to be "Wanderer above the sea fog" by Caspar David Friedrich.

Harry Dresden, Chicago's only professional wizard, accidentally travels to Equestria after being attacked in the Nevernever. Twilight is none too amused with their newest 'guest', but trouble is brewing. Somepony is planning something sinister and the mane six may need Dresden's help however little some of them want it.

Story Image by: Lynxgriffin
Cover arrangement by: Novel Idea

This story is a sequel to The Dresden Fillies: Strange Friends

Almost a year has gone by for Harry Dresden since he left Equestria. He'd have written, but between saving his newly discovered brother and destroying a scourge of vampires he's been a little busy. Then out of the blue he receives a strange letter from Twilight asking him to return. With no cases at the moment he eagerly accepts, but his friends aren't the only ponies expecting him. There's been a lot of rumors since his last visit and some ponies aren't too keen on seeing him come back.

A sequel to The Dresden Fillies: Strange Friends.