This story is a sequel to Mission: Improbable

A few weeks after the Spy returned from his extended stay in Equestria, the Medic found that he needed to have a few of those so-called "ponies" to... study. But with robots still attacking Mann Co., how can he find the time to acquire such a specimen?

By sending a scout ahead, of course.

It had been about a month since the changeling incident in Canterlot. Everypony is on edge, because stray changelings keep popping up here and there, trying to blend in with the population. Everyone worries that one of their closest friends, or even their family, could not be who they appear to be. But what happens when a pony isn't really that pony...

...but they're not a changeling, either?

Finalist and judge's top choice in Equestria Daily's 2012 Nightmare Night contest.

Fluttershy has been plagued by nightmares, and Twilight wants to help her get rid of them. But when the bookish mare begins to pry into the depths of Fluttershy's unraveling psyche, she finds more questions than answers. What do her dreams mean? Why won't they stop haunting her? And why does the creature she keeps seeing inside them seem like more than just a simple night terror?

For two years I've been hiding, for two years I've tried to just live my life. But it all came crashing down the day I chose to have lunch at a Diner. Now I'm forced to run again, forced to leave the life I tried to build. But what choice do I have, what choice does a mere clone have when she shouldn't exist?

Twilight Sparkle is reading a book she can't seem to put down. It's not even a very good one, as the author keeps on writing directly to the alicorn. For three days now this is all she has done, as her friends desperately try and find her. Oddly, the author of the book knows more about Twilight than most... even if their only goal appears to be her death.

The star system Omega Centauri was just another oddity on a map to scientists in the not too distant future. However when they found the star was orbiting an earth-sized, earth-like planet instead of a black hole as its motion had suggested, a mission was scrambled to investigate this most unusual of celestial behaviors.

Hamstrung by politics, and nearly crippled before it began, the 'Lone Ranger' mission was reduced to just one crew member and left to his own devices.

These are the logs of Arrow 18 and its lone commander. This information is classified TOP SECRET by the Global Space Agency.

Do NOT tell the princess.

Alone in the nothingness, a mare waits.

Edit: now available in Chinese!

Spike led Thorax into the throne room of the Crystal Castle confident he could convince the others that the changeling could be trusted. That he meant no harm, and instead wanted to be an ally and live peacefully with them. That he could make them see Thorax for what he really was. That they could befriend the changeling and accept him as one of their own.

They didn't.

And consequences followed.

SPOILERS IN COMMENTS!
First featured on 11/12/2016. -- Now with a TV Tropes page. -- Review by Arcanum Phantasy -- Review by PaulAsaran

Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.

After finding Discord hiding out in his closet, Twilight Sparkle soon learns the most horrible of truths about herself and the world surrounding her.

And then she learns another truth.

And another. And another. And...