So, my idea is to add a mode to sandbox that you can switch on or back off. Playing in this mode would appear normal, but as time went on, natural disasters would take place, such as floods, earthquakes, volcanic eruptions, ect.
These events would be triggered when it rained, but only a small amount of the time, maybe a 1/20 chance or something. Anyways, when this event is triggered, rivers would burst their banks, making the tiles around them have a small amount of water on, like a puddle, but as it kept raining the sea level would rise, as well as river tiles would increase, and this would happen for a range of 5-10 days, which would be the same amount of time it would take for the floods to recede. During the floods fish would be able to swim up the river and any tile which is deep enough for the swim icon. If left on land they become dead and nichelings can collect them. You'd get a notification when the flood began.
This would start with a block of raised water like the river in the sea, and there would be no notifications. it would slowly grow until it was many blocks long and a few wide. after a few days, it would sweep across to the island at night before the player has a chance to move their nichelings, and sweep any it catches (none on the high ground or in the centre of big islands!) and deposit them many tiles in a particular direction. they could be left in a different part of the island at best, or deposited in the sea itself at worst. The only notification a player would get would be one after the tsunami struck. If they are observant, they could spot the tsunami forming and move their nichelings to a safer place. If a tsunami hits a nut tree it could easily make it a tree stump, and any other entities such as bearyenas, rabbils and nuts would be washed away too. Berry bushes would be reverted to their destroyed state.
This rare event could be triggered completely randomly, and it would cause the geography to change ever so slightly in height sometimes. The notification would be given before, the day of, and after the event. When there is an earthquake there would be a 50-25% chance of a repeat earthquake, with the maximum being ten. The most dangerous aspect of this event, however, is that it can trigger eruptions and tsunamis.
These could be triggered by an earthquake on a mountainous island or by itself. You would get the very topmost block disappear, and be replaced by lava which would turn by turn move 2-3 blocks in rivers down the mountain. Any nicheling that steps in it instantly perishes and the lava sets fire to any grass around it. Berry bushes or trees in its path are destroyed fully as are animals. Nichelings within two blocks experience added heat and nichelings within three blocks start taking damage, like sickness. after a few days, the lava starts to cool off and leaves blackish tiles which are very fertile and have a low chance of spawning a destroyed berry bush on them. they also tend to grow grass (re-growing usually) and spawn many roots.
I hope you like my ideas, I'm sorry if some of them have already been suggested!