MLP/Undertale crossover.
Not a PWNY-verse story.

Long ago, the Monsters and Humans fought a great war. The Monsters lost, and were sealed in the Underground. It would take the power of seven human souls to break the barrier that kept them imprisoned. They only had six. And so the Monsters waited and hoped, praying that another human would find their way to the Underground. Some thought the seventh soul would give their King the strength to break the barrier. Some dreamed of a human who would be their friend, and save them all...or had nightmares of one who would bring back the war.

...but nobody came.

...but somepony did.

Eons after the war, with no way to tell how much time had passed above, a tiny blue filly with wings and horn fell into the underground, calling for her Mama. None knew the poor creature's nature or origins...but her soul was powerful with magic, even more so than a human soul.

None can know what will come...of this little 'Woona'.

Cover art by Sanyo21

Twilight Sparkle, Sunset Shimmer, and Moondancer are the top students in Celestia's School For Gifted Unicorns. One is a dedicated bookworm with a love of learning, other is an outcast full of ambition, while the last one just wants to enjoy life... a lot.

Connected with unlikely friendship, together, they fight crime live their lives, one day at a time.

(Sometimes they fight crime, too)

While it is set in Stallionverse, knowledge of previous stories is not required (you'll miss a joke or two at worst).

Teen rating and sex tag for slightly edgier humor, innuendos and Moondancer.

Guest chapters provided by the ever talented Eyeswirl the Weirded. You can't hug him through internet (you can try), so give him love by checking his stuff- quality guaranteed.
My own chapters are edited by the ever kind and generous Docontra, whose patience knows no bounds.

Time after time, through chaos and through wars, Princess Celestia prevailed.

Of all the terrible forces she could have fallen to, Flim Flam Industry was the last one anypony had expected.

With thanks to gardrek for editing (3-6) and PinkieDP, Ice Star, and Odd_Sarge for prereading help.

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!)

The princess's fanatical student. A startlingly honest bootlegger. A prissy high-class escort. A traitor caught between two loyalties. A hyperactive pyromaniac. A quiet assassin who can kill with a word.

The night that has covered Equestria for a thousand years might just be coming to an end. And all of these familiar faces will be engulfed in the war between a victorious Nightmare Moon and her sister, returned from a millennium of exile.

Even as the sun rises, the situation has never seemed so dark.

This story was edited, preread, and otherwise improved by Einhander, Comrade Sparkle, CartsBeforeHorses, Spigo, and IR Pony.

[This story has been rewritten, link to it is here ]
Canterlot is getting ready for the wedding of the century, Princess Mi Amore Cadenza is marrying the Captain of the Royal Guard and part of the draconic royal family will be in attendance. In addition to helping prepare the most high profile wedding Equestria has seen in living memory, Celestia has tasked Sunset Shimmer and the rest of the Elements of Harmony with befriending the future queen of the Dragon Empire and her entourage, the first Sorcerer the Empire has ever had. One thing is certain, this will be a wedding that nobody ever forgets.
(New description has be made by none other than DoomManta)

(Story has been inspired by This picture) Go check out the person who did it Zig-Word

New cover art is drawn by http://akerabronzpaw.deviantart.com/ It may say a different name but same person.

Note to all: This story has been made before the season 6 ep 5 "Gauntlet of Fire" was made but may have some details about it. ;)

Also this story got Featured, a lot... thanks everyone xD

Twilight was bored.

So very, very, bored. Hopefully somepony will give her a decent challenge somewhere along the way, but...so far, all it takes is one spell.

Just one.

And she was very, very bored.

Twilight Sparkle has come across the impossible. A book she's never read before, with an odd plus-like shape emblazoned on the cover. What is this book, and what does it mean for Equestria?

Meanwhile, Isaac has been stuck in the basement for a long time - centuries? Millenia? But when he finally finds a way out, will he be able to adapt to the planet that's moved on without him?

Crossover with 'the Binding of Isaac : Rebirth', a game by Edmund McMillen.

Rated Teen, because somebody can't keep it polite.

Featured on 5/31/18!

Check out another great tBoI crossover, Binding of Isaac: Beyond by IAmNotSmartest!

When Twilight Sparkle was just a kid, her best friend was a girl named Sunset Shimmer. Though their friendship had a bit of a rocky start, they quickly became inseparable, no matter how much everyone thought of them as ‘weird’. They were there for each other.

Were.

Years after the tragic accident that tore them apart, Twilight is determined to move on from her loss, and she sets off on an independent research project to investigate the strange happenings at Canterlot High. Little does she know that she will soon come face to face with what appears to be a literal ghost from her past.

Coverart by Kare-Valgon. Chapter illustrations by Zorbitas.

Edited and Pre-read by Dubs Rewatcher, r5h, and Kalan.

Takes place after Rainbow Rocks, but was written before Friendship Games and does not take it into account.

Chinese translation

Print copies now available.

[ Inspired off Season 5 Finale - Nightmare Moon Verse ]
Social reject, blank flank, and failed candidate for Celestia's School for Gifted Unicorns, Twilight Sparkle's life couldn't get anymore depressing even if she tried. Yet still she looks to the other things in her life to get by, such as her job selling donuts at Joe's Bakery, her best friend Smarty Pants, as well as her inspiration to someday be as great as The Great and Powerful Trixie herself! Life isn't as bad as it may seem, and she enjoys the simplicity of her daily routine, the peace of her recluse world. That is until suddenly she is targeted by the current ruling body of Equestria, Nightmare Moon herself!? Perhaps she spoke too soon. Better run Twilight, destiny is calling!