A group of humans attempt to escape a global nuclear war through the use of time travel. However, something goes wrong with Sam Mitchell's pod, flinging him far into the future, into a time where humans no longer exist and a race of sentient ponies now thrive as the dominant life form. He eventually comes to the attention of a certain purple unicorn, who aims to learn all she can of Sam and his civilization as well as help him adjust to his new life.

Can Sam handle living as the only human? Can Equestria, and Twilight in particular, handle the changes this alien brings?

Going up to the roof for some fresh air after pulling and all-nighter, our "hero" makes the mistake of closing his eyes for a bit.
When he opens them again, he is no longer on the rooftop in Copenhagen he was expecting to be on... no he's somewhere very different, and extremely unfamiliar.
How will he react? How will the ponies react? Nothing is certain, except for one thing...

He never asked for this.

This story takes place about 8'ish years after the second season of MLP:FiM, the language of Equestria does not match any earth languages (that the main character knows of at least), and the human in question knows nothing of these ponies or the world of Equestria.
He emerges into Equestria on the roof of a building in Manehattan, not the Everfree, not Ponyville and certainly not one of the princesses' bedrooms in Canterlot Castle.

Oh! Spoilers in the comments and all that jazz, not gonna go into a whole spiel about it.

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.

After a brief spat with Spike over a seemingly trivial matter Twilight decides that in order to learn more about dragons she should try to become one. With a simple spell she transforms her little pony self into a larger dragon and quickly realizes that she has no way to change back available to her....