The first story in The Journey of Graves.

Ponyville is getting ready for the arrival of Princess Celestia's marshals, elite of royal guard and travelling heroes of the people. But in all the hustle and bustle of party preparations, a lone traveler slips into town, a young man with business concerning Twilight Sparkle. What that business is remains to be seen, but you can be sure Ponyville won't make it easy for him.
After all, where would be the fun in that?

I always wanted to go to Equestria. When I got the chance, I took the deal without reading the fine print. To my surprise, I didn't arrive there as a pony, or even as a human. It seems I get to view this world from a different perspective than what I've imagined.

My name is Echo. I am a Diamond Dog.

-Edited by the one, the only, Nathan Traveler!
-(Cover by Jovial_Shake of fimfiction.net)
-Now featured on Equestriadaily.com!

Twilight Sparkle wakes up one morning to find she's undergone some changes. She shortly discovers she wasn't the only one. (New cover art by Jamey4 on deviantart http://jamey4.deviantart.com/)

Warning, this work of fiction contains multiple fourth wall breaks, massive silliness, and more than a trace amount of alicorns.
The author may or may not have snapped at times in the writing of this work, and it shows. Bring a towel, you may get wet.

On the night of her return from exile Nightmare Moon comes across resistance as she had expected. However she had a backup plan on hoof for just such a predicament, tearing off a small fraction of her soul and attaching it to the bearer of the element of magic. Now she must play the long game to ensure that she can obtain the loyalty of her new host and once more rise to power over Equestria.

Cover art thanks to Tonto the trotter.

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

Two years after Nyx was stripped of the Nightmare's power, Twilight Sparkle is attempting to raise Nyx as a normal filly. But as Nyx's magical abilities begin to grow out of her control, the pair quickly earn the attention and ire of some powerful ponies who do not have Nyx's best interests in-mind.

During the night, the Elements of Harmony mysteriously vanish, and Princess Celestia enlists the aid of their bearers to find them. Twilight is forced to choose between her duties to her princess and her duties to her daughter. In the process, she discovers a web of conspiracy surrounding her daughter that reaches back a thousand years into Equestrian history. Will Twilight be prepared to face the things she learns along her journey's path: about Nyx, about Celestia, about Equestria, about the Elements...

...about herself?

Based on Past Sins by Pen Stroke Pony.
Alternate universe, because Twilight never became an alicorn or princess in this story.

Vinyl Scratch is always up for a good party! But when she partys a bit too hard, even for her standards, she wakes up in a mysterious place with no memories of how she got there, and only the soft sound of Fur Elise to greet her listening ears.

One would think that the wounded Trixie would appreciate Twilight Sparkle taking her in to nurse her back to health. But for some ponies, leaning on someone else isn't so easy. Their crossing of paths sets them both on a journey that neither of them would've expected...

We all wear a mask called composure, beneath which hides a heart that twists with guilt and hidden feelings. Regal as she is, Princess Celestia is no exception. What might be revealed should circumstances cause this mask to slip - or break?

Set several years after the potential conclusion to the series.

For almost a thousand years, the immortal Nightmare Moon has reigned over Equestria as Empress. To the average pony, Nightmare Moon is an overarching enigma whose rule is absolute and whose wrath is terrible. But to Twilight Sparkle, who as an orphan has never known her parents, the Empress is something else entirely. When the young unicorn is brought under the royal wing as an apprentice, she learns a great deal more about the supposed tyrant than she ever knew. But as Twilight is introduced to life with her new mentor, she is thrust into a world of political intrigue, conspiracies and secrets. Secrets that were never meant to be revealed. As allies and enemies plot against the very peace of the nation, will Twilight fall prey to the perils of her new position? Or will she prosper and find in Nightmare Moon the mother she never had?

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My eternal gratitude to my editor, LordOfTheWrongs, without whom Night's Favoured Child would not be the story it is today.

Now with added TVtropes!