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 Secret Histories

“To the precious peace-loving ponies of Equestria:

Has your life lost meaning in a world without Princesses?

Have law and order in your quaint little village collapsed under an endless onslaught of monsters and brigands?

Do you need a hero? Do you dare to be a hero in these dark and uncertain times?

Fear not, little ponies, for if you are brave enough, there is something you can do: Travel to Hoofington and spend a night at the Inn of the Prancing Pony.

I guarantee if you do, your life will change...forever.”

This is a story set hundreds of years before "The Best of All Possible Worlds", yet it was written after and influenced by the events of "Parade Coverage" and "Secret Histories". It was co-written with Hope. The cover illustration is largely taken from part of the fan art "First Day", by Harwick.

The "Alternate Universe" tag is because this story explores a different way that the events following the banishment of Nightmare Moon could have unfolded. As for the "Human" tag...well, that will become clear later.

After the changelings' failed invasion of Canterlot, Twilight tries to soothe some of Ponyville's rampant paranoia by casting a spell to prove there are no imposters hiding in the town. But her spell leaves her in an alien body, facing a mob of angry ponies who just don't believe her when she says she is Twilight Sparkle.

Or, at least, she was Twilight Sparkle, anyway...

Featured on Equestria Daily, 2/17/13
Cover art is by the awesome and amazing Conicer

Comet takes his job too seriously. Angel doesn't take anything seriously.

Comet joined to protect kingdom and princess(es). Angel joined for adventure and danger.

Comet isn't interested in mares. Angel can't stop talking about stallions.

Comet is a pegasus. Angel is a bat pony.

Together, this unlikely duo goes through life as Royal Guards from basic training to fully fledged guardsponies. Who knows? Maybe they'll even start to get along.

Cover art by slawomiro.

This story is a sequel to Past Sins

Hearth's Warming is a time for friends and family to come together, celebrate harmony, and welcome the new year. Nyx is looking forward to just this as she rides the train to Canterlot with Spike and Twilight. She's going to meet her extended family for the first time and wants nothing more than to make a good impression. Yet, the sheen of the holidays can't hide the trouble caused by meddling grandparents, relentless reporters, and a paranoid uncle.

Strange nightmares are plaguing the ponies of Equestria.

Somepony must help ponies to face their deepest fears, but unless Princess Luna is able to discover who—or what—is responsible, the nightmares may never end.

Scootaloo is ready to prove that she can be as fearless as her big sister, Rainbow Dash, even if it means never having a peaceful night's sleep again.

I'm lost, but I don't know where I'm from.
I miss them, but I don't know who they are.
My name is Rainbow Dash, but I don't know who I am, or what happened to me.

And I don't know if I'll ever be the same again.

Editing provided by LoyalLiar, Ruirik, and Mooretis. Cover art also provided by Ruirik.
Russian translation provided by Athlete; you can find it here.