In this behind-the-scenes explanation of the Mare in the Moon incident, follow Nightmare Moon and Princess Luna as they encounter strange, artificial beings from another world. A Portal 2 crossover. Contains two stories:

Of Cores and the Alicorn: After what seems like an eternity, Wheatley and Nightmare Moon cross paths and discuss their respective exile in space.

Guerrilla Corefare: Nightmare Moon is free, but the magical accident that released her did more than just send her back to Equestria. Now, from behind the scenes, Luna exploits Nightmare's newfound weakness in order to sabotage the plans for eternal night.

Note: As older stories (in fact, written before the debut of Season 2), these are fairly amateurish, relatively speaking, and contain speculative-at-the-time characterization for Luna. With the exception of a few minor edits, however, they have been submitted in their original forms for posterity's sake. This isn't Airstrip One, after all, and I don't work for the Party.

Fluttershy's kindness to all creatures is legendary in Ponyville. When a freak storm blows in from the Everfree Forest, however, she and her friends discover the limits of compassion, and the dangers of living with your heart wide open to the world.

After Rainbow Dash loses a wing in an accident Twilight finds herself to be the only pony capable of restoring it. But can she reconcile the month long treatment with her suppressed feelings for the pegasus?

I wanted to change a lot in this story before submitting it here, but then it took longer than expected and I had other things to take care of. So, after only the most basic revisions, here it is in all its imperfect glory. And in chapter form, too.

Cover image by me.

Skipsy also made a comic for it.

Pinkie Pie is overjoyed when she meets a Pegasus who seems almost exactly like her.
She's fun, silly, and Pinkie's friends take an immediate liking to her.
What could possibly go wrong?

Translated into Russian here!

There comes a time in every growing dragon's life when he has to go visit the doctors. Twilight just needs to show him who's boss... hijinks, as they say, ensue.

Each of the chapters of this fic is an independent story featuring one of the Mane Six having an encounter with the supernatural. They are presented as one story because of their common theme. The stories are:

Fluttershy: The Curse of the Night When Angel falls sick, Fluttershy ventures into the Everfree Forest at night to find a remedy. Though she faces danger, she escapes... but not unchanged.
Rarity: Blood and Water You know the story. Rarity gets seduced by a creature of the night, and her friends don't realize what's happening until it's too late. They find the vampire who turned her and destroy him. But then what happens?
Rainbow Dash: The Big Battle Discord's defeat didn't erase every trace of his influence on Equestria. Fortunately, hard-working ponies are already gathering the remnants of his power into Manehattan for easy disposal. What could possibly go wrong?
Pinkie Pie: Gallows Humor Pinkie Pie, Ponyville's premiere prankster, is dead. So why haven't the pranks stopped?
Applejack: One of the Herd Applejack may be in charge of Ponyville's biggest farming community, but that doesn't mean she can't take a break now and then. Besides, tonight's meteor shower should be even better than last night's...
Twilight Sparkle: The Case of Wild Clover the Warder It's a boring day in Canterlot, and Twilight Sparkle has time to kill. Maybe picking up an old lot of books will brighten her mood.

Feedback and error-spotting welcome!

Nightmare Moon has won, and the world has been shrouded in eternal night. But hope still lives. The land of Equestria is currently divided between the armies of the usurper and those of the Dawn Militia. However, the greatest danger to the rebellion may not be the dreaded Mare of the Moon, but her lieutenant, Eclipse–formerly known as Twilight Sparkle.

This story is a sequel to Silent Ponyville

In an attempt to make her feelings known, Fluttershy begins to persue the target of her delicate heart's affection. However, when her interest seems to be oblivious to her feelings will she find the inner strength to admit her true feelings to the one she desires? Or will disaster follow her at every turn? (Takes place 1 month after Silent Ponyville, but is not required reading material)

Sequel: http://www.fimfiction.net/story/4868/Silent-Ponyville-2

Rarity's genius at fashion design is unparalleled. But when she tosses off a design for a caprese, just to get the CMC out of her hair, she's shocked at the popularity of the simple garment. Its success threatens to undo her carefully promoted image as a designer of high fashion.

Winner of the /r/mylittlefanfic Writing Stravaganza.

After spending most of her time studying indoors throughout the winter season, Twilight Sparkle is given a new assignment by Princess Celestia: to form and lead Ponyville's new EHL team, the Ponyville Golden Leafs. Twilight and friends lace up their skates to take on the EHL's elite in hopes of winning the Celestia Cup with teamwork and friendship.