Instead of preventing them from going up by physical barriers, perhaps you could set up some kind of negative effect of being above ground? It have been a while so don't remember the mechanic exactly but something like mystcrafts scorched earth? And then when you want them to go up you give them some sort of protection against it.Ok I guess people can just stay under water... That will be a challenge, I wonder if I should make sponges easier to get
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Maybe the "ozone" equivalent layer is gone and the ground has been flooded in radiation? And the water is the only thing that stops the radiation(rock doesn't absorb it).