The Princesses find an alien creature barely clinging to life at the scene of a terrifying crash. Can the Combined Power of the Elements of Harmony save it, or more importantly, should they save it? Will the arrival of this strange creature tear Equestria apart?

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https://tvtropes.org/pmwiki/pmwiki.php/FanFic/Article2

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