MLP/Skullgirls Crossover. Contains Skullgirls Spoilers.

A weapon lands in Ponyville. A living weapon. Bound and changed, she fought her world's gravest threat. Now she's free, for all the good it did her.
She is called Painwheel: a raging monster with the heart of a little girl. Will she find peace? Or more tragedy?

Ladies and Gentlemen(?), it's Showtime!

Twilight, Applejack, and Rarity have a sleepover. Certain uncomfortable secrets come to light.

Thanks to Einhander and Exuno for their help.

In the aftermath of her battle against Tirek, Twilight Sparkle is unwell. She wants more. She needs more. And she is afraid of what others might think of her.

But even in the midst of her growing despair that she has betrayed everything she stood for, she learns something about friendship and what it means to be an alicorn.

This story is a sequel to What Have You Done?

Chrysalis, the Changeling Queen, has taken her prize, unhindered by Equestria's precious heroes. Celestia is little more than another prisoner of war now. The Bearers of the Elements of Harmony are lost, and the Elements themselves have turned away from Equestria's plight. As the world they once knew begins to crumble, a single question is asked among the people as they look up at their fallen heroes.

There is no such thing as "miserably ever after," for someone will always be fighting for things to change. Hope doesn't die just because someone's turned off the lights. Truth doesn't vanish when deceit begins its reign, and Harmony can only shine brighter among chaos.
Even as this world falls, we'll work to build it up again.
Even as you lose yourself, you can find greater things within you.
Even as fear rises up like a tidal wave, we'll forge a sanctuary to stand against it.
Even as you break, someone will always be standing there next to you to carry you through it.

Cover art is by Odin-odin.
Story theme (Equestria in Grey) is by Omnipony.
Main Characters are Twilight, Velvet, Discord, Nightlight, Luna, and Chrysalis, in that order.
See you in the comments, my dear readers.

Twilight Sparkle has had a crush on Princess Celestia for a very long time. When Celestia's own advice prompts her to confess her attraction, Twilight discovers a secret that Celestia has hidden for hundreds of years. With the fires of the sun itself separating them, can Twilight find a way for them to come together?

Cover art by NadnerbD

Huge amounts of editing by Jordanis

Twilight Sparkle's tenure in Ponyville has been anything but calm. Since the Summer Sun celebration, she's dealt with a variety of foes, from Nightmare Moon to dragons, hydras, Discord, and King Sombra. But when Pinkie Pie asks for help with a small problem, Twilight finds herself pulling out all the stops to deal with the most dastardly (and curious) fiend yet encountered: Sugarcube Corner’s haunted mailbox. Rainbow Dash’s letter from the Wonderbolt Academy is on the line. Failure is not an option.

Rainbow Dash knows one thing for sure, she is definitely not a barbarous, uncivilized dolt who doesn't know polite conversation from a hippopotamus's rear end. And also that she's definitely not the one who's wrong. Rarity is wrong. Rainbow Dash is absolutely, totally, a hundred percent sure of it.

But then why did Rainbow just buy a wagon load of apology bouquets?

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!)

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 an unsettling experience with Soarin, and hearing that her friends think she's gay, Rainbow Dash starts to question her sexuality.

When she finds out the truth, will it jeopardize her relationship with Soarin and perhaps her friends?

The "Sex" tag is for language. This is not a story about being gay or not gay, but on uncovering one's identity and coming out.