I used to love the idea of a human getting to visit Equestria. It sounded like a good way to set up so many shenanigans, except it's plagued with boring characters or really cliché ones or... the dreaded Sue.
I never expected it to happen. For real.
No, that's not real. What am I saying? Tom's... missing. Yes, and I will find him. He's not in the show... that's ridiculous. Don't say such things! My little brother can't be part of the show! It's just a coincidence that this little alicorn showed up, spoke with his voice, has the exact same personality and is based on his personal design for his alicorn OC!
IT'S NOT REAL!

What am I supposed to do now?

When one unbelievable event happens, nothing is considered impossible anymore. For one unfortunate human soul, he must find answers to an unlikely truth to understand just what makes the fictitious, a reality. What is in store for him unfolds one thing at a time, and if he thought it couldn't get any stranger, he might have to rethink his whole life.This misfortune becomes something of an rewarded experience, but this gift can also be his curse.

As for Twilight and Lyra, they are prepared for anything out of the ordinary, ...well almost.
The search for answers is motivated by curiosity and interest that may lead to unpredictable outcomes.

Cover Image self-arranged with vectors from deviantART
Vector credit:
http://chromadancer.deviantart.com/art/What-the-fu-246722708
http://redpandapony.deviantart.com/art/Twilight-being-Skeptical-296460108
http://90sigma.deviantart.com/art/Shocked-Princess-Luna-294402582
http://jennieoo.deviantart.com/art/Huh-292228127

Okay, I don't know if anyone can hear this, or read this, or whatever, but I'm trying my best to use Pinkie Pie's legendary fourth-wall-breaking powers to try and get a message out.

If you can hear this, I need help. I'm in Equestria, and man, this is strange. But I'm also stuck in Pinkie Pie's body, for some reason.

Yes, it's just as weird as it sounds. And now, I need your help... because all the ponies in this town think I'm crazy!

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

With Twilight Sparkle still adjusting to life as a princess, Rarity becomes convinced she can help her friend by finding her a special somepony. And when that somepony turns out to be Fluttershy, awkward dates and adorable moments are sure to follow!

Cover art by mocha-creme (Thanks to OminousBrony for the suggestion!).

For a different take on the same characters, be sure to check out my RariTwiShy story, Our Lady's Courtship.

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

Off shoot of: My Little Pony: Friendship is Magic - Off the Record.

After several nights filled with horrible dreams, Rarity comes face to face with the dark side of her soul in her sleep, as it attempts to convince her that she is truly a horrible pony on the inside.

During this battle within Rarity, the entity that once controlled Princess Luna takes notice of her momentary weakness, and decides to use the opportunity to seize one of the Elements of Harmony, as to guarantee her safety from being sealed away once again.

However, the overflowing dominance from Rarity and her dark side, starts to crawl into Nightmare's mind, making her question whether or not she should continue with trying to conquer Equestria, or perhaps take a different route.

Cover art here! It was money well spent!

http://jinzhan.deviantart.com/art/Nightmare-Rarity-440977340

Cuddles meet crusades, and hilarity ensues.

"The pieces are set, and the dice are in play. But does every pony have the heart for this day?"

Nearly two hundred years have passed since Rarity Belle merged with the Crystal Heart and took the throne of the Crystal Empire. Since then, through her care, determination, and vision, the Empire has flourished like never before. Now Empress Rarity stands as not a ruler of a providence, but the monarch of a rising superpower.

Today though, is the Empress' Birthday, and Lady Merry Sapphire, seneschal to the Empress, is determined to make this the best birthday Rarity has ever had. Little does she know that not everypony shares her enthusiasm for today...

Notes:
This is an official prequel to the Princess Twilight Sparkle's Birthday stories, created by Autumnschild. This story will develop and expand much of the world we made, but taking place 250 years before PTS500 and its sequel, PTS505. Due to its time gap and status as a prequel, you do not need to read the stories created by Autumnschild, and I have done my best to help that. However, knowing what happened in them will help you be a bit more aware of what is going on, and I encourage you to go read them for they are very enjoyable.

We now have our own group! Come check out the Birthdayverse!

Credit goes to Autumnschild for the proofreading for this story.
Razalon The Lizardman is credited for the grammatical overhaul.

Great thanks goes to these two, for this story would not be as good without them.

This story is a sequel to Princess Twilight Sparkle's 500th Birthday

Five years have passed since the events of that fateful morning. Smarty Pants and her friends set off on an adventure of a lifetime to discover the secrets of the past when they awaken a… oh wait, that would be spoiling it!

Many questions from the first story will be answered! New questions will arise. Lunch will be had, pies will be thrown, blood will be kept inside bodies because seriously, ew blood, you guys.

Notes:
- Cover art commissioned by HAK2. Check out his other stuff, too.
- This is a story in the Birthdayverse.
- This story was written and completed (except for the epilogue) before Season 4 of MLP:FiM aired.
- Many thanks to my faithful Pre-Reader and all around super-duper best pony, Blood Lord go read his story, too!