Unconscious NPC spawns in on the edge of the map, "So-and-so wanders into your village, wounded, exhausted and starving after being split from their group in a battle. Give him medical attention and send him home."
Or for NPCs with no faction, "after narrowly escaping a bandit ambush"
Toxic fallout
Replace with something magicky that requires you to either hole up inside, or avoid certain areas of the map. Might be difficult to implement an affliction punishment like toxic fallout's buildup and subsequent cancer risk.
Solar flares
Ithildien lamps malfunction for a day
Everybody gets sudden spooky magical weariness and cannot craft/craft slower than normal (which should be just as annoying as unpowered workbenches in vanilla)
Ancient danger
Instead of a room full of cryosleep caskets or mechanoids, just spawn dwarven stronghold walled rooms and throw in piles of treasure, good armor, and possibly dragons
Psychic events
Uhhh.. magic?
Tornados
Bring them back, they're just too infuriating not to have
Currently can't do this event when it comes up, because trade beacons are not available, but it is a useful and lore-friendly quest. I'd suggest requiring you to bring silver to an outpost of the faction that has the information or something similar.
Transport pod crashes
Toxic fallout
Solar flares
Ancient danger
Psychic events
Tornados
Other ideas?