The pre-Cataclysm Earth didnt manage to resist blob, the Old Guard cant resist blob, the Exodii gave up a long time ago, what makes you think MC will be able to?
I think late game should be like tetris late game, the game slowly becomes more and more hostile but doesnt really change fundamentally, only the ability of player to react to hostility slowly wanes. As time passes factions slowly expand and what used to be vast wilderness and ruins peppered with enemy outposts here and there becomes big patches of hostile land with narrow strips of neutral or contested ground in between. Blob is lorewise the big bad so eventually it prevails over all, consuming all biomass into humongous amorphous slimes as big as mountains. The aliens will flee, the mycus may form cocoons to hide from blob, the triffids will burrow through the ground or something, the player will be left to roam barren land with what food remains preserved in his deathmobile and using irreplaceable ammo and plutonium cells for his power armor just to stay alive, besieged by monstrosities 24/7, desperate for sleep. All those attempting to farm or build lasting settlements will have to spend tons of ammo daily to gun down waves of swarming horrors just to get their harvest of cabbage out of land they defend. Early game is easy because you live off the stuff left behind by billions. Late game you must sustain yourself with far less against far more.