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?

There was only one explanation. For all of it. All of the strange, erratic behavior. Her irrational fear of the sun. Her nocturnal habits of locking herself in in the dark and closing all the blinds. Wearing her sunglasses everywhere, even inside! It was time to invest in some silver, garlic, and a wooden stake.

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