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

When Twilight invites Rainbow Dash to come stargazing with her, imagine her surprise when she accepts the offer. But as the night wears on and the stars come out, it becomes apparent that the pegasus has something on her mind.

[Takes place pre-S4 finale.]

Through unknown means, Sombra amassed an army and launched an attack against the Crystal Empire and a changeling sub-hive. This forces Celestia and Chrysalis to meet, and agree to a temporary alliance between their kinds. Neither is happy about the situation, but for the lives of the ponies and changelings they lead, they are willing to do what is necessary.

Yet, as weeks and months pass, the pair find working together is not as horrible as they originally believed. Is a lasting peace, and perhaps more, possible between ponies and changelings, between a princess and a queen?

Written for Equestria Daily's Super Happy Hearts and Hooves Lovefest Fanfic Event

Twilight Sparkle has a secret. Not one that can change the world or overthrow the Princesses. But it is one that hangs over her head every day. One that colors her every thought and action. Or at least, that is how it seems to her. But when a rainbow colored pegasus asks her out on a date, will she learn to see past it, or will her secret tear apart a budding relationship?

Inspired by the excellent fic Asylum by Daemon of Decay.

Takes place before "A Canterlot Wedding."

Thanks to SilverSugar for the cover art. You can check out her other works here

This story is a sequel to The Celestia Code

When the monsters created by the dark crystal engine escape their prison, it's up to Princess Twilight Sparkle to deal with them. She gets help and advice from Princess Luna, but things don't go as planned. In fact, when a pony who relies on logic and rationality tries to navigate the stormy seas of emotional entanglement while simultaneously saving Equestria from a horde of evil creatures intent on destroying everything they encounter, nothing goes as planned.
AUDIOBOOK by VisualPony
WARNING: Major spoilers in the comments.

Book 2 of the Alicorn Adventure series.

Goodreads Page
100% Approved by Twilight's Library!

The Badass Twilight tag applies more than ever, but please note the new tags.

This story is a fairly direct continuation of The Celestia Code. You might be able to follow it without having read The Celestia Code first, but it's better if you do.

The sequel is here: The Twilight Enigma

Most excellent pre-reading/editing done by the erudite AcademicPony and the dapper statoose!

After nearly being mugged Twilight turns her considerable talent with magic towards self defense. When a fight with Luna goes farther that either of them wants it to, Twilight will need to find redemption in her new position as Luna's bodyguard and stop a conspiracy that wants to bring back a force more dangerous than either of them.

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

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 Past Sins

In the wake of the battle with Tirek, Twilight Sparkle becomes fixated on restoring Golden Oaks Library. After all, it was home for her little family of three. But as her attempts to repair the books and tree continuously fail, her friends must take matters into their own hooves. Discord, as the good friend he is, tosses Twilight and her extended family into an unexpected adventure while Twilight's other friends get to work on the new crystal palace.

All together, they'll do everything to ensure Twilight and her family have a place to call home when they reach the end of the road.

Long before Twilight Sparkle was taken under the wing of Princess Celestia, another pony was given a chance to prove himself. Your history books will tell you that he was a bitter, lonely, powerful old Unicorn who never really understood the magic of Friendship. But history, as we all know, only ever remembers one side of the story.
This is the life and the tutelage of Star Swirl, one of the greatest pony minds to ever walk Equestria.

Featured by Seattle's Angels on July 6th, 2014.
Featured on Equestria Daily on September 23rd, 2014.