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 The Sword Coast

The shadows of the past plague the present.

Twilight Sparkle stands on a precipice, one false step from a dark destiny. Months ago, she set out to find her foster father’s murderer. After she defeated the Black Knight, she was hailed as a hero, but what she remembers most is the lives she took. On the path of strife, she discovered more about herself than she ever expected.

With her friends by her side, Twilight sets out for Canterlot, seeking the villain responsible for the death of her father and the crises that plagued the Sword Coast. On the way, a sadistic spellcaster interested only in power intercepts her and promises to unlock her potential. In the aftermath, Pinkie Pie is taken captive by the secretive wizarding order that rules Canterlot.

Twilight’s journey takes her through the doors of a prison and into the depths of a forgotten place. She encounters horrors made from nightmares and soul-stealing beasts raised from the black of the Abyss, but what she fears most is the monster within. How far will she go to save her closest friend?

Featured on Equestria Daily
Cover by Bluest Ayemel
"I love this fic. Keep it up!" – Sethisto (on the EQD page)

Side stories: Tales of the Sword Coast

Warning: Comments contain spoilers. Proceed at your own risk.

This story is a sequel to Memoirs of a Royal Guard

From the outside looking in, life has never been better for Silent Knight. He is the first pony in a long line of Royal Guard ancestry to earn a commission, he has a loving mare by his side, and he bears the kingdom’s highest honor for bravely risking it all to protect Princess Luna. The future shines bright with potential, but the shadows of the past lurk at every twist and turn that lies ahead.

Guilt, anger, and regret are constantly at war in the depths of Silent Knight’s mind. Despite his best efforts to enjoy the life he has, he finds himself trapped in the past, reliving the moment when his unit was ambushed and his ponies were killed. He refuses to show any weakness, instead hiding everything behind a tough face to protect himself and those he loves. But his true feelings—and what he plans to do with them—shackle everything he holds dear with chains forged in secret.

Secrets of a Royal Guard is a comedy series with romantic, dramatic, and adventure elements. It features an original character cast and their interactions with the princesses they protect. It is recommended that readers be familiar with Memoirs of a Royal Guard.

Quill & Blade Universe

This story is a sequel to Days of Wasp and Spider

Believed dead by their creators, the ponies that will become Celestia and Luna have broken their mental conditioning and escaped into the wilderness. Here they plan the revolution that will free all ponykind, knowing that it is only a matter of time before their ruse is discovered.

Back in their underground arcologies, the ponies' erstwhile masters deal with the consequences of the escape, all the while unaware that something lurking at the bottom of space-time wants them all dead.

A Soot-Covered World, book 2.
Canon species only/no humans.
This story has nothing to do with the Holocaust.
Art by InLucidReverie, used with permission.

When a dark enemy begins hunting the young wizard Twilight Sparkle, the walls of the fortress library of Candlekeep cannot protect her. Not even her mentor, the archmage Star Swirl the Bearded, can keep her safe. With a price on her head and the shadow of death on her heels, her only hope for salvation is the Magic of Friendship. Perhaps, with powerful allies at her side, she can find answers and uncover the truth about her destiny.

(This story is inspired by the Baldur's Gate CRPG series by Bioware, but you do not have to be familiar with BG to understand its events)

Featured on Equestria Daily
Cover by Bluest Ayemel
"I love this fic. Keep it up!" – Sethisto (on the EQD page)
"From it's fantastic character development of Twilight and fast pace and exciting action, The Sword Coast is an excellently written and well thought-out story." – Amy Clockwork

Side stories: Tales of the Sword Coast
Sequel: Shadows of the Crystal Empire
Warning: Comments contain spoilers. Proceed at your own risk.

This story is a sequel to Culling of the Hives

It's been twelve years since Twilight awakened as a changeling. With Phoenix Roost's focus on economic and population growth, the hive has grown strong.

The rest of the changeling hives have been ravaged by war for years with Twilight's brood remaining aloof. Sphinx psyker immigrants have dispersed throughout not only Equestria but as far as the Griffin and Minotaur nations, eager for a new life away from the paranoia of their homeland.

Yet for all of Twilight's desire for leave the rest of the queens to their wars, the Home Guard's proclamation will force Twilight to return to the jungle of her rebirth.

Real cover art pending.

As always, big thanks to Boldish42 and A Bitter Pill for editing.

Everypony has a story. Some tell of heroic feats and grand adventure. Others tell of villainy against the forces of Harmony. The story of an average guard, however, is one of obscurity. They live in the background, unnoticed but ever-present.

Silent Knight assumed his tale would be like that of his father's: join the Royal Guard and serve Equestria. He would be just another helmet and spear, part of the rank and file. And that was all he ever wanted.

However, when Captain Shining Armor asked for volunteers to form a House Guard for the recently returned Princess Luna, it was Silent's hooves that stepped forwards to set his new life in motion.

This story is a sequel to Stardust

Everyone knows the story of Hearths Warming Eve. They know the tales of the three pony tribes and how their strife brought the Windigoes upon them, and how the Fires of Friendship saved them from their frozen fates. For countless generations the tale has been told, but how has it changed over those years?

Or is any of it true in the first place?

Only one pony knows, and Celestia would prefer that the past stay forgotten.

(Based on a 'What If' line of thought that was born from the Stardust storyline. While some familiarity with Stardust and Mente Materia doesn't hurt, this story can be enjoyed on its own)
(Coverart available soon from the amazing FoxInShadow!)
(Many thanks to Arzoo, BradTheBrony, Vandenbz, and Setokaiva for prereading!)
(Complete with it's own TVTropes page as part of the Stardust continuity)
(Character tags will be added as chapters are added!)
(Possible spoilers in the comments! BEWARE!)

Inexperience is a foreign concept to Celestia. At least she thinks it is. Right up until the moment a rash decision leaves her with a student who is a dozen years younger than what she's used to.

Enjoy.

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!