Read the blog post about the Gifs Alex posted on Twitter. 
If you read between the lines, something big and bad (and most likely technologically arcane in some way) is coming. Anything biological in nature? Could be. Could not be too. We'll just have to find out!
I would bet an
enormous sum of money that the "something big and bad" has something to do with the dimension Phase ships dip into. In the description for one of the phase weapons or ships (I forget which), I believe it is implied that something potentially sinister lives there. If I remember right, at least.
Also, while we're at it, I bet the Domain is still out there and that they won't take too kindly to independent interests (even factions parodying them like the Hegemony) taking control of a Sector that once belonged to them.
And that is all on top of the general decay of civilization in the Sector and the potential threat of the [REDACTED].
The apocalypse is getting crowded, my friends.
Reminds me of Dark Souls; either the Age of Fire ends, Demons wreak havoc across the world, or the Abyss and rampant humanity consumes everything. Lots of end-of-the-world scenarios. I wouldn't mind seeing Starsector go in a similar, bleak direction.