First of the Savage Skies series.
After running afoul of timberwolves in the Everfree Forest, Fluttershy is saved by a mysterious young colt with a most unusual and disturbing feature. Realizing that he is alone, without anyone else to care for him, Fluttershy realizes that she must try to bring this lonely foal out of the forest and give him a life of love and friendship. The problem is that this colt's...unique qualities have made him more than a few enemies, including some who are closer to home than Fluttershy realizes.

Now with a sequel: The Promise of a New Day.
Now with a TV Tropes page.

This story is a sequel to Shadow of the Sun

Story 5 of the Savage Skies series:
Autumn has arrived in Ponyville. The harvest is in full swing and all is as it should be. After enduring the trials of the past few months, Dawn Lightwing is looking forward to what promises, hopefully, to be a peaceful season before a tumultuous winter. However, the coming season has the unwelcome effect of bringing his enemies closer than he feared. However, he is fortunate to have a loving family, good friends, and somepony who is maybe more than just a friend.
The series begins in Foal of the Forest.
Now with a TV Tropes page.

This story is a sequel to Storm on the Horizon

Story 4 of the Savage Skies series.

It is well-known that the brighter the light, the deeper the shadow. Princess Celestia is unquestionably Equestria's brightest guiding light. Unfortunately, two ponies must deal with the very deep, very dark shadows that she casts.

Dawn Lightwing has overcome many trials since moving to Ponyville. However, his past and the ponies that haunted it are not as far behind him as he would like to think. Whether he likes it or not, his enemies, who draw their hatred from their irrational reverence for Princess Celestia, have found him again and he must struggle with the fact that his mere presence could a threat to his friends and his new family.

Twilight Sparkle must deal with a different shadow as she travels to Canterlot in order to learn more about the mysterious Eyes of Nightmare, as she must contend with the Noble Court, who live in the shadow of the Royal Palace itself, its members planning to use Twilight and her friends to advance their own ambitions, stopping at nothing to have her under their influence.

Thankfully, neither of them will have to deal with these obstacles alone.

However, something even more dangerous is stirring. Dark matters are afoot.

The series begins with Foal of the Forest.
Now with a TV Tropes page.

Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.

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!)

Sweetie Belle gets stuck in a time loop.

Traducción Española: https://www.deviantart.com/spaniard-kiwi/art/Un-poco-circular-1-4-990271915

Proofread by many people such as: 0_0, refferee, Leonzilla, crooked, TheGreatEater, and other people I may have missed.

Five years ago, Dr. Natalie Sydney was contacted by an enigmatic extraterrestrial. Now, it's happening again.

This story was written for Equestria Daily's More Most Dangerous Game writing contest. It fulfills the My Little Dashie-inspired prompt. It was 11th-hour-proofread and edited by Nicknack.