Maybe a path of progression that would be available at world creation could help?
Maybe instead the vanilla survive-until-you-die could be set into a mode, with a story mode alongside, where the player goes for the endgame goal of "fixing, " the cataclysm, either by finding someway to destroy all enemy factions or making peace, like an idea above said, Try and make a treaty with the migo, or find a way to make the mycus sentient enough to where you could speak with them and compromise on sharing the world. Then, the faction you make peace with would then work alongside, you, Suddenly, a migo showing up might be a godsend rather than a another body to the pile if you were being attacked by a horde.
If this would make the game too much like a player-driven world, then have factions other than your own team up with enemies, like the merchants or bandits teaming up with the gracken to find tech from our world, slowly converting merchant or bandit locations into technologically advanced utopias. Then, you would have to raid them for something a faction you are allied with needs, creating full-on war between factions. Cataclysm then turns from survival in the wild to political survival, dodging assassins that would be tailored to your fighting abilities and current weapons and juggling relations with the various lifeforms slowly colonizing earth.
Heck, make mutants a faction, where you have to achieve one of the mutation thresholds to join, making it impossible to join or even talk peacefully without looking like a bipedal mosquito.
I’m new, so I apologize if this seems… I dunno, uninformed. Thanks for reading.