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

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

(New readers, unsure where to start? The Education of Clover the Clever is best.)

The stars can see the future, and they don't like what they see.
Beset by signs of a great evil approaching on the horizon, Princess Luna and a young unicorn who speaks to the stars set out to uncover and prevent an unknown disaster.

Star Swirl the Bearded: the greatest wizard nopony has ever heard of. Why is that? What did he do? Why do so few now remember that he existed at all, and why do those who do remember him say he was one of the most important unicorns of all time?
A mythical retelling of Equestrian history.

23.02.2014 Featured on Equestria Daily!
Prequel to a more popular and completed sequel, The Education of Clover the Clever. Feel free to read either one first.

Cover art by VSabbath, used with permission.

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

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?

This story is a sequel to The Crown of Night

Now available in print from Lulu.com! Hardcover - Paperback.

(New readers, unsure where to start? The Education of Clover the Clever is best.)

Clover Cordelia is a freshmare student at the Cambridle Academy of Magic who is determined to become a great sorceress.

Star Swirl the Bearded is a legendary wizard in need of an apprentice.

It's a tough job, working for the world's greatest wizard. On top of the usual challenges of student life there are apocalypses to deal with, and assassins who show up at inconvenient times, and plant life scheming for world conquest.

It's probably nothing Star Swirl can't take care of, provided he and Clover manage to resist killing each other first.

Previously updated alongside its prequel, The Crown of Night. It is not necessary to read The Crown of Night first.

Featured on Equestria Daily!
Featured on the Royal Guard!

Cover art by iisaw.

"Characterization is the name of the game here, and this story's take on Star Swirl is one of the most enigmatic and intriguing I've seen. His eccentricity is offset perfectly by his straight mare, Clover the Clever, and the interactions between them are a joy to behold."
-Prak, PR for the Royal Guard.

Rated "Why Haven't You Read These Yet?" by PaulAsaran.

Weird praise for The Education of Clover the Clever from the comments:

"........The sadist in me is grinning while the student is screaming it's little lungs out "
-Smirkythread.

"I can't tell if he's insane or not. And it's glorious."
-FancyFan.

"I am unsure if this is merely silly and deranged or subtly brilliant."
-SIGAWESOME.

"Ok, so I like this story. I actually like it quite a bit. I have no clue why though. Not a single clue.
I haven't a clue what you're doing right, but keep doing it. You're awesome."
-Vibrato con Amore.

Twilight is invited to Canterlot to compete with some of the greatest magicians in the world for the Moonstone Cup, a prestigious award for the most powerful and skillful magicians, unicorn and otherwise. Can she win? What sort of competition will she face?

Awesome cover image was taken from NoOneBahtim

Some things in this world happen by chance. Others do not. Twilight Sparkle is about to learn a disturbing truth that will turn her world upside down.

- Originally written May 2011 for Deviant Art

Reading this story first is strongly recommended:
(Blood is Thicker) http://ciroton.deviantart.com/gallery/26378692#/d3e1ndq

Credits:
~Image by JohnJoseco~ ~Edited by BrotherPrickle on Deviant Art~