A/N: I've been kicking this around for a while, but I only got around to writing it just now. There will be more, and there will be slash.
Graffiti found on the ruins of the Bikini Bottom bank:
War never changes, does it?
Two hundred years before present, the unknown denizens of the land waged violent and terrible war with weapons unknown to the ocean dwellers. Most of these ocean dwellers did not and could not know of the terrors of radiation and the fallout that blanketed the land and fell or was swept into the oceans; they only knew the effects.
Some fortunate creatures, mostly those around the old nuclear test sites, had enough ingrained resistance to radiation to neither succumb to mutation nor die altogether. And unfortunately, not all those who succumbed died.
For some even more seemingly fortunate creatures, there were the vaults. Funded by an unknown entrepreneur for reasons unknown, they were scattered across the sea floor, near pre-war cities. They were designed to be self-sufficient refuges, impregnable to anything their designers could imagine and advertised as a peaceful, affordable getaway, or a shelter should anything untoward happen under the sea.
Little did the residents of these vaults know that they were really being used as test subjects in a series of ocean-wide experiments, designed to study how the various sapient species would react to stress and isolation in the event of a total disaster; others were used to carry out illegal tests on live people. Still others, few and far between, were left alone as control groups.
When the few sea dwellers who knew anything of land life heard the news about the war, they started a panic that almost killed more people and caused more destruction than the actual bombs would; looting and riots were widespread, and the vault dwellers retreated into their refuges and locked the door against any and all newcomers. Those unfortunate enough to be trapped outside fought over basements, caves, and other shelters, no matter how minimal.
Many died, but some survived - presently, two hundred years after the bombs fell, undersea life has begun to claw its way back towards civilization, resettling the old cities and building new settlements with materials gathered from the ruins of the ancients' civilization. The greatest threats to these settlements and to the caravans which wander the sea floor are hostile wildlife, raiders, and the radiation which now permeates both land and sea.
The land around the ancient city of Bikini Bottom, termed the Atoll Wastes by its inhabitants, was ironically enough less hard-hit by radiation than other parts of the sea bottom, even supporting minor agriculture in places. The city itself lies mostly in ruins, but here and there a few buildings are almost intact; its population, numbered in the lower hundreds rather than the pre-war thousands, has managed to band together collectively build a fence around the city as a deterrent towards raiders.
Living in this post-war desolation is difficult and often dangerous, but life goes on, as best it can.