I think what the author is trying to convey is that humankind cannot evade responsibility for environmental damage, no matter how hard it tries.

The gigantic hole, which over the years has become a dumping ground for every kind of garbage, has come back to haunt society. For many years, people thought that whatever they didn't want could be safely deposited in the hole and that they'd never have to deal with it or worry about it ever again. Out of sight, out of mind, as they say.

But the reappearance of the pebble at the end of the story, the very same pebble that was the first item put into the hole, indicates that society may be able to run from its past but cannot hide. Sooner or later, how we treat the world in which we live will always come back to haunt us. If we see the environment as just a thing, an object of exploitation that exists purely and solely for our benefit, then at some point we will have to pay for what we've done.

And it's the same in the story. People treated their environment with contempt, as if it were nothing more than a giant trash can. But what goes around, comes around, and that little pebble dropping from the sky is the harbinger of a severe backlash from Mother Nature.