It's not real, it can't be real. Ponies are just cartoons and some fanfics on the internet. The wings, the hooves... I'm just having a bad dream!
I wish that were true. But pain, friends, and a strange drink are telling me this is all too real. I'm a pony now and I think the world is falling apart.
People, the end is nigh, the world has decided to go out with a bang, and it's taking us along for the ride.

*Loosely based on "The Conversion Bureau" universe.*
*Note about the art. Chatoyance was very kind to create some fan art. Just as a little note though "John" has brown hair not bond. Just a little tidbit to keep in mind while reading. Thanks so much again Chatoyance!*

Have you ever had a dream that just seemed so real, that it was impossible to say for certain that it was even a dream at all? A dream that, despite all of its impossibilities, seemed to re-write your entire perception of reality, re-writing your sense of what—and indeed, who—you are? Accepting change is hard enough as it is. But when you're a somebody who wakes up as a somepony, how do you cope with the impact such a drastic change has on your mind and body? With changes like these, it must surely just be a lucid dream—albeit a suspiciously accurate one—just brimming with potential and ripe for exploration. So you might as well suck it up and make the most of these distressingly…unusual circumstances, and seize this psychological adventure before you wake up and the dream ends.
After all, this couldn't possibly be real, so the dream must come to an end eventually…right?

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

Violet is a girl who has lived her life about as normally as a girl can. When she lived among humans, she had friends, went to college, trained to be an actress. But when Equestria appeared off America's Pacific Coastline, the entire world shook with the repercussions. Years later, Violet lives in a pony occupied Albuquerque, one of the last humans in the Western United States.

It's been a long time coming, but Violet has finally decided to give up her humanity, but her decision leads her down a dangerous route that is anything but magical.

So Equestria is now eating up our world. Humanity has only got a couple of years until Earth is gone. You either get busy trotting or you get busy dying. People have got a lot of changes to make in those short years.

The creator having a metaphysical nightmare, the race to save technology, the last TV specials anyone will see. These are just a few of the tales that will lead humanity on the path to a strange new world.

Spin-off of Reality Break