One wintry evening, a frozen, half starved and exhausted mare wanders into Ponyville from out of the wilderness. It seems straightforward on how to deal with her, a traveller from a world of humans across the forbidden Void, on an adventure in Equestria. Welcoming her, the Element Bearers try to befriend this mare, aid in her quest, and help her find her way home again.

Things don’t quite work out as planned.

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