It's been three days since the Equestrian Railway Service incident, and things are finally calming down in the wake of the Dusk Guard's first mission. Three days since the team's first mission came to a successful conclusion. Three days since their first trial by fire. Three days since Sky Bolt, the team's engineer, had everything she'd created put to the test. And it all worked. Nothing went wrong.

So why can't she sleep?

First of the Side Stories to The Dusk Guard: Rise. Familiarity with Rise is not required, but recommended.
Side Stories so far:
Carry On
The Definition of Strength
Old Habits
Emoticon
Remembrance
Trust

The Saga has a TV Tropes page!
"This is 100% Approved by Twilight's Library!"
Added to Twilight's Library 12/5/2013
Featured on Canterlot's Finest
Special Thanks to Sonorus, Jorlem, Sinister Voice, Templar22 and Bronze Aegis for their help pre-reading and editing.

Stranded on a hostile, alien world, Twilight Sparkle and Rainbow Dash must depend on one another and a fellow alien castaway if they want to return home to Equestria.(originally published on FFN)

Eighty years after the events of The Dread Chitin, Equestria is a radically different place. The arcane science of the late Duran Thirk and the information found on the Star League library core have combined to catapult the nation's science ahead by hundreds of years.

Now, facing the possible aggression of a completely unknown alien power, Twilight Sparkle and her friends have to gather together once more, leading a crew of the best ponies they could assemble in a voyage outside their own star system. They seek to learn about their potential foe, to explore the galaxy around them, and possibly find allies and friends to stand alongside them. Who knows what they will actually find?

For most of Applejack's life, she didn't know what she was. True, she understood who she was well enough.
But ponies don't change shapes, nor do they get strength from love.
Applejack never thought too hard on it... until the events of a certain wedding brought about some harsh realizations.
Now, with Equestria still reeling from the surprise attack, will Applejack manage to come to terms with what she is? Will she even be able to keep her secret safe?
For if the royal guards don't get her first, the conspirators in the shadows just might...

Image provided by Heilos -

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey

This isn't where I belong. I left all this behind years ago, moved on with my life. But a mare from my past brought me back, and now she won't let me go. So I'm stuck here, trying to make the best of it with ponies that don't understand me, don't even like me. But when something moves in the darkness, and when things go wrong in the cold, dead night, they'll turn to me to try to set things right.

Why? Because once a police pony, always a police pony.
~~
This is a spin-off story to 'Why am I Pinkie Pie?!', and will contain spoilers for that story, but it's not necessary to read that story to understand this one.
Cover art by the talented Conicer
Need more Cinnamon Swirl? Merlos the Mad wrote a fanfic of this story!

There is now a side-story: A Hard Day's Nightmare Night

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!

Celestia leaves to deal with a foreign crisis, giving her sister a chance to rule alone and become more attached to the modern world. She calls on Twilight Sparkle to advise Luna, hoping her student will be able to draw Luna out of her shell. With two major threats to Equestria already defeated in the past year, it seems like the perfect time to let Luna gain some confidence and experience in the modern world. After all, what are the chances of a third disaster occurring?

Now comes with complimentary tropes.

This story is a sequel to Stardust

Times are changing for Equestria as Twilight’s return brings with it news of people and cultures from beyond the peaceful world everypony knows. Aid and volunteers are freely offered to help the besieged humans of Earth because every Equestrian knows that’s what good friends do. Unfortunately, making friends can also have the unintended consequence of making enemies.

When the monsters besieging the humans strike at Equestria with a level of brutality not seen in over a thousand years, the cry for help is sent to all the kingdoms of the world. Honored allies step forth to fulfill ancient treaties and oaths. Enemies, old and new, bury their grievances. An alliance never before seen in Equestria will be created to combat the monsters from the void.

And because of these events, a grim but welcome sibling to the XCOM project is born.

(XCOM/FiM Crossover)
(Sequel to Stardust, which I recommend reading before starting this. Fortitude Amicitia and Broken aren't required reading but are supplemental to the storyline)
(Gore tag for blood and violence)
(Alternate Universe tag because of the divergence from canon that Stardust has caused)
(Uses elements of Season 4)
(Coverart produced by the amazing Carnelian!)
(Many thanks to Arzoo, BradTheBrony, Vandenbz and Setokaiva for prereading!)
(As of 03/07/2016, the prereading team consists of Arzoo, BradTheBrony, Noble Cause and Metallusionsismagic!)
(Complete with it's own TVTropes page as part of the Stardust continuity. Could use some updating!)
(Character tags will be added as chapters are added!)
(Featured 5/12/2014! Thanks folks!)
(Possible spoilers in the comments! BEWARE!)

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!)