Daring Do is a wealthy and famous adventurer with a loving husband and an adorable daughter. She lives in a brownstone full of old treasures and relics. She also has a sister.
Ditzy Doo is a post officer who used to be a brilliant engineer, used to work at a university, and used to have a husband. She isn’t bitter over her sister’s success; she’s happy with her life. Mostly.
When the two meet up in Vanhoover with their families, old arguments begin to repeat worse than ever when they become affected by a pair of ancient daggers. It may fall to the ones they love to keep them from murdering the other— possibly literally.

Death tag for ancient assassinations, homicidal thoughts, and the slow decay of all things.
Violence tag for the lead-up to... all of the above. Also, ghostbusting.

Traveling between parallel universes is impossible, especially during the process of regeneration, but the Tenth Doctor doesn't have time to question the facts. He's just been thrust through a tear in the fabric of reality, gotten a new body, and landed on a planet called Equestria. Specifically, he's landed in the worst possible place in all Equestria – somewhere that's ready to unleash a “big ol' storm of chaos”.

That's just the beginning of the Doctor's strange new lease on life: there's a whole host of mysteries to explore. Who is Derpy Hooves, the gray pegasus who understands more about him than even she knows how to explain? How does Princess Celestia already know him? And what's the truth behind the Order?

Above all, the Doctor needs to discover if this new universe can heal the wounds he suffered in the last. Only one thing is certain: there's an awful lot of running left to do.

(Warning: For those of you who haven't watched up to the Doctor Who episode 'The End of Time'... spoilers. Also, this story begins between Seasons 2 and 3 of FiM, and things start to... diverge from there.)

Side stories can be found at The Merely Mundane Tales (of a Mad-Pony in a Box).

After a mirror portal field trip being conducted by Luna goes terribly wrong, Ocellus finds herself trapped in a strange palace far from home. That palace, once abandoned, is now infested with a hive of love-starved changelings intent on using her only way home as a means to invade her world.

Otherwise, Ocellus appears to be alone.

At first.

The story is inspired by, and a homage to, my favorite game of the last decade. However, this story is neither a crossover nor AU. This story is set after "The End of the End" (but before "The Last Problem"), and is purely a My Little Pony story. Warning: rudeness and intolerance are not allowed in the comments, but spoilers are. Exercise discretion. Remain polite and on-topic. And please enjoy the story!

When balefire and death rained from the skies, many took sanctuary in the giant underground shelters known as Stables. However, those who could not make it to one of the many Stables set sail for the Summer Sunset Islands. They hoped that the tourist hot spot would be spared the devastation. These refugees soon faced a sheer wall of violent weather, known today as The Storm Wall, sealed them away from the rest of the world. The refugees were forced to live their lives on the high seas of Oceania.

Two hundred years later, a tribal seapony has a chance encounter that would change life in Oceania forever.

Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

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!)