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!)

No one alive today can say where she came from; simply that she has always been there.

And yet, few ponies have had a greater impact on Princess Celestia's life than Raven, her most faithful aide.

Inspired by and based off of a headcanon put forth by Heir-of-Rick, though perhaps a bit less insidious than what he had in mind. He very kindly provided an alternate version of his image for me to use as my cover image! Text added by me.

All comments and criticism very welcome!

Featured in the Royal Canterlot Library! Go there to read the interview for some behind-the-scenes info on this story!

Translations: Chinese, Spanish!

Thrust headlong into a strange new world, Solaire of Astora must make amends before he can continue with his mission. Unbeknownst to them all, a shadow from his past approaches.

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?

============

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!

My name is Twilight Sparkle.
I am three hundred and seventy five years old.
Except for Spike, all my friends are dead...But not for long

Betrayed by Celestia, and isolated in her castle with only Spike for support, Twilight Sparkle enacts a powerful spell to reincarnate the element bearers through her own body.
Her friends will be reborn, and, with the trials of being a mother to her friends ahead of her, an unraveling secret from the past following her at every turn, and the possibility of a brand new life so close in reach, Twilight just might be reborn too.

Credit for both the inspiration for this story and cover picture go to
Crystal Leviathan

One year after her coronation, Princess Twilight Sparkle is dead, killed by her own subjects out of fear and jealously. After the funeral, Princess Celestia isolated herself from the world, mourning the loss of her brightest student and daughter figure.

But she cannot weep forever. She must take control of her duties once more. Haunted by the memories of the assassination, and its aftermath, Celestia slowly makes her way to Twilight's resting place to find some closure.

Now With its own TV Tropes Page!

Sequel is up

A thousand years ago, Princess Celestia banished her sister to the moon, that much we know. What wasn’t known, and what Celestia kept secret was that before her banishment, Luna had given birth to a foal. Now a thousand years later, as Nightmare returns to Equestria to bring about Eternal Night.

Twilight Sparkle, protege of Princess Celestia, struggles against the tyranny of this ancient foe. But how will she be able to save herself and her friends when the truth of this ancient legend crashes down upon her? Twilight will have to confront herself...and her heritage.

Polaris501

"My name is Lyra Heartstrings, and you will not remember me. You won't even remember this conversation. Just like with everypony else I've ever met, everything I do or say will be forgotten. Every letter I've written will appear blank; every piece of evidence I've left behind will end up missing. I'm stuck here in Ponyville because of the same curse that has made me so forgettable. Still, that doesn't stop me from doing the one thing that I love: making music. If my melodies find their way into your heart, then there is still hope for me. If I can't prove that I exist, I can at least prove that my love for each and every one of you exists. Please, listen to my story, my symphony, for it is me."

Cover pic by Spotlight: askspotlight.tumblr.com

After a long time--she would be more precise but Twilight has lost track of time--she emerges from the dark of the library. Her candles are burnt down to nubs. There is no food left in her pantry and furthermore, no coffee. So she goes to seek both.

And finds the town changed. Or is it Twilight who has changed?