A couple weeks after her first Nightmare Night in Ponyville, Twilight gets lost in the Everfree Forest all by herself, hoping to find a way back to town. As Twilight searches, she comes across a strange flower that sprays out some strange pink pollen. She inhales it, and gets a pain in her stomach. The pollen made her pregnant with a colt that looks like her male counterpart from another dimension (Dusk Shine from On a Cross and Arrow by Conner Cogwork).

Meanwhile, a kid who has been living with his abusive aunt and cousin make his life miserable when his parents are working in Europe. That young boy keeps getting treated like a slave, and barely gets any food. They even force him to clean up the house that they keep messing up, no matter if he was healthy or sick. Then one day, he gets really sick the day his parents come home, unexpectedly to the abusive aunt and cousin. He had a sickness that couldn't be cured. At least he saw his parents one last time before he passed. He then wakes up as the colt that Twilight Sparkle had given birth to.

When you wake up naked in a strange bed you can feel uncertain. When the person asking how you feel is a ‘talking horsie’ you can find it hard to focus on anything else. When they seem so unimpressed when they already have talking Cows, Sheep, Diamond Dogs, Zebras, Dragons, River Serpents, Buffalo, and Minotaurs then you might as well just keep your head down and do farm chores and try to gradually get used to this all.

But when three infamous fillies ask you to do something then perhaps would have been better to say ‘no’ and leave your life quiet and uneventful.

Set from sometime not very long after Discord’s puppy-eyes and reform to where I gamble and have the season 4 opening threat dealt with on the day of the coronation and Equestria Girls start only two days later.
(EDIT: Though from the spoilers/teasers it seems the vague references to the threat missed by so far as to obviously be referring to something else...)
(EDIT 2: Blog post on problems and thoughts. AU tag added since things were contradicted.)

In Manehattan there is a strange ape-like creature that is being held in a lab. Its injuries bear the distinctive marks of illegal sport hunting by exotic game poachers.

What's strange is that there's an entire section in books on natural life about this creature designating its kind maned apes. What's even stranger is that there are accounts throughout Equestria's history about maned apes turning up.

The maned ape, given the moniker Big Red by the scientists holding it, is given over to the crown and transferred to Ponyville for safe keeping. The Mane 6 comb through Equestria's historical texts and oral account to try and find where the maned apes come from.

This is an HiE story that starts in Season 1 shortly after Apple Buck Season.

EDIT: 6-8-2022 Featured! Woo-hoo!
18-202023 Featured! Woo-hoo!

Ugh.
Alright, do you want some advice?
Don't go evil if you don't want to have heroes trying to kill you repeatedly. I know, sometimes you have to do things that are morally questionable, but at others, just be a good guy. Wait in line rather than summon a horde of undead to tear the throats out of everybody except the barista. Or just freeze everybody in place. That's at least funny in a conventional sense.
I'm (sort of) reformed now.
Unfortunately, there're these six mares and their ruler who are making this VERY DIFFICULT.

EDIT: After four days, the Featured streak has ended. It was a good run.
EDIT: Featured again on 10 May? Aw, stahp it guys. Stahp.

EDIT: New coverart courtesy of Leila Drake. Go to her and commission stuff.

For as long as she could remember, Strix has lived in the depths of the infamous Everfree Forest, the lone owl-pony resident of its shade and gloom. As an omen of ill fortune, as well as her unique appearance, she's since become an myth that parents tell to their foals to get them to behave, something that Strix is not overly fond of. Tired of being alone, she ventures to Ponyville to find acceptance, and hopefully, a partner that will love her for who she is.

Written for the 1st Monster Mare Story Competition (Unpopular Monsters) Contest

A one-winged Pegasus blacksmith named Swage sets up shop in Ponyville. An old wound has left him grounded, but his heart still belongs to the clouds. When he finds Scootaloo to be a fellow grounded Pegasus, he takes her under his wing and brings her along on his quest to fly again.

Featured in Twilight's Library.

This story is about Martin, a 17 year old teenager that ends up in Equestria. The one responsible for all of this is Discord. There will be hardships to overcome and unknown plots by Discord to disrupt, but it will all boil down to one choice, The Choice.

Mesa gots prereader: Tsaukpaetra
Will add tags and ponies as they come up in the story.

In our lives, we are presented with many choices, and these choices define our very existence. You can choose to be evil, you can choose to be good, or you can choose to walk the line between good and evil. I too have had to make choices in my many years of life, some I wouldn't take back no matter what, and some I would give anything to reverse, but probably the biggest choice I've ever been presented with, the choice that changed my life, for better and worse, was the choice to come to Equestria, and become a pawn in a very deadly game.

I am Shadow, and this is my tale.

Set in the Chess Game of the Gods universe created by Rust and Blackwing

Greetings weary traveler/bored reader. Let me regale you with my tale. The tale of a mere mortal, with nothing particularly special to his name, brought to a magical land of dragons, minotaurs, griffins, and of course ponies. But he came as no mere human. He came as the epic warrior, the manliest of swordsmen, that most dashing of multiverse travelers, the mighty Gilgamesh! What adventures will this powerful and magnificent warrior find in his travels? HELL IF I KNOW! LET'S STRAP IN AND SEE WHERE THIS GOES!

Looking for cover art if anyone's interested.

Crossovers with:
The life and times of Xante, Baron of the Frozen Wastelands, First among Liches, Lord of the Dead, and Fabulous Rainbow Magic User

Golden Graces, Headless Headaches

I Will Hunt You Down

A Thousand Tortured Souls Scream My Name

Gravity of the Situation

Land of Friendship and Magic

And Then There Were 10… Er… 67

Son of Invention

Ten Against One

Time Ticks On

Let's Just Say That Umbra Really Needs to Put a Lock On His Diary

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May 25, 2014: I GOT FEATURED! HOLY CRAP THANK YOU SO MUCH!

Spartan III Theodore-G172 Wyvern-Two
Status: MIA
Last deployment: Reach, Orbital Defense Platform Power Station Delta
Mission: Defend ODP Power Station Delta from Covenant Ground forces
Mission Status: Unsuccessful
Equipment: Modified SPI-ES Armor, BR55 battle rifle.
Wyvern Team status: MIA
With the fall of reach many Spartans were active in the beginning and end of the defense. Many lost their lives in the hope of saving the planet. They failed.
_______________________________________________

The Changeling hive launched a desperate attack on Canterlot to save themselves from extinction. It failed. With the whole world now knowing about them they have no choice but fight for their very survival. Outmatch and outnumbered, they have no hope of survival. They fight for precious land to give the hive more time for an effective solution or war ending strategy that will save them. With Equestria hell bent of the destruction of the hive this seems unlikely. All seems hopeless. They need something to deliver them hope.