It occurred one peaceful night. Half of Equestria awoke to the sound like a double-shot thunderclap. A percussion heard in the skies and rattling windows from Apploosa, to Canterlot, to Ponyville. Nopony knew what it was or what it heralded for the world as it drew a line across the nation.

For Twilight Sparkle, this isolated incident might have faded from memory after a time, if not for the strange rumors of a creature sitting on the hill on the outskirts of town.

These are her thoughts given written form. These are Sparkle's Notes.

Report EVERYTHING to the Princess.

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