After an accident that Rapidash has only a hazy memory of, she finds herself in the company of an odd blue Ponyta. With no clear way home she has to adjust to this new world and find her own way back.

Taken from here
and added background and name by Lilith911.

Several weeks after recovering her crown from Sunset Shimmer, Twilight Sparkle discovers she can communicate with her counterpart from the other world, who has finally arrived at Canterlot High. When Celestia theorizes that the portal can be re-opened, Twilight and her friends--as well as the OTHER Twilight and HER friends--decide to trade places, so they can learn more about each others' worlds. The only catch: neither party can return to their own world for a full thirty moons...

This story is now cancelled. Its concepts will (eventually) be retooled into (Mis)taken Identity.

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!)

Twilight, Applejack, and Fluttershy arrive... somewhere after a teleportation spell goes awry. Stranded in an unknown land with nowhere to go they hope to find somepony that can help them find their way home. They find something else instead.

Edited by the wonderful Isaac3924! Go thank him for making my stories readable.

Rainbow Dash's pet, Tank, was killed by a unicorn, who decided a lighting spell was best to practice in the open.

How can she live with this injustice? How can she live with her unicorn friends?

How can she live without Tank?

Edited by Roarbox

When Dialga and Palkia start to attack one another in Alamos Town, a Ponyta named Flare Blitz is caught in the crossfire. After falling into the dimensional rift, he finds himself in a strange new land filled with brightly coloured ponies. Flare doesn't know how he got here or if he can even get back home...

The question is, will he even want to go home?

Edit: So I finally got offa mah flank and started the re-write. I want to give massive props to Blazinblade7 for editing as well as my little bro, who is teaching me a great deal of authory stuff.

You can find the TV Tropes page here!

Thirty moons of annoying bragging from Rarity.
Three years of jealousy and annoyance.
Sweetie Belle was fed up.

Ever since the historic battle of Twilight Sparkle and Sunset Shimmer 3 years before, Sweetie Belle had been curious beyond words. How could such powerful magic exist in the universe? How is there a world of equines?
"It's the magic of friendship darling," Rarity said countless times.
That answer never satisfied her.
One afternoon, Sweetie Belle discovered that the fabled magical portal had reopened for the first time in 3 years. She called her two friends, Scootaloo and Applebloom, and explained the news to them. They were unbelieving, but decided to travel with their best friend into the portal. When they got to the other side, they were indeed in Equestria, but it wasn't what they expected. It was a tragic world of disharmony.

Vaati the Wind Mage has grown bored with the whole villain thing. He's trapped himself in a cycle doomed to repeat itself forever. Seeking a way to escape this miserable cycle of escape, kidnapping, and defeat, the legendary sorcerer inadvertantly teleports himself to another world entirely; a world populated by talking magical ponies who believe friendship is magic. Just how will the former villain survive this sugar bowl of a world? Will he end up learning a few lessons in friendship himself? One thing's for sure, retirement has never been this exciting.

AUTHOR NOTE: This story takes place in an episodic format. That is, it follows the style of the show in that every chapter is an 'episode', hence why they will all be lengthy. Some episodes will be canon ones with Vaati along for the ride, and others will be original where Vaati takes center-stage. The first episode takes place shortly after 'Griffon the Brush-Off'. Vaati is from Legend of Zelda and is property of Nintendo. You already know who owns FiM.

Dark machinations are at work, and for Rarity, life has taken a turn for the worst. She's now in a place called Ancelstierre on another world, where nopony has ever seen or scarcely even heard of a unicorn before. What dangers lay in wait in this new land of strange magic and mystery? What happened to Rainbow Dash or Pinkie Pie? More importantly, how does she get back home?

Welcome to the Old Kingdom, my little ponies. Magic works quite differently here...

Fox squirrels are frisky little creatures. Ferocious too, as Fluttershy will come to find out. However, like many of Equestria's own little critters, they react best to kindness.

Kindness is what Fluttershy needs the most now, too. Dark machinations are at work, and she's become trapped in a foreign land where there are very few things familiar to her. Lost and frightened, she will travel these worlds, fraught with perils and dangers that seem to be never ending; hoping to one day find a way home.

Credited Authors : Cold Spike, FormlessDream