The author is commenting on the tendency many of us have to take the Earth and the environment for granted, doing damage that we cannot even begin to understand. The people in the village and the neighboring city think that they can throw nuclear waste down the hole they find after a tsunami knocks down a local shrine. They are comforted when they are told that "there would be absolutely no above-ground contamination for several thousand years and that they would share in the profits."

So, the people do not know what the potential hazardous effects could be below-ground, and they feel better when they think that neither they nor their children, nor their children's children, will have to deal with the fallout from their actions. They are being selfish and short-sighted, preferring to make a profit now rather than think about the safety and well-being of future generations.

When the voice and the pebble, very much like the voice and pebble that went into the hole at first, seem to come from somewhere else, the author seems to suggest that everything we do to the Earth is immediately connected to some consequence and repercussion. We may think that there will be no short-term consequences to the things we do to the planet, but we have no way of knowing that. We continue to take it for granted, and, the author seems to suggest, we will end up reaping the consequences of our abuse of it sooner rather than later.