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The “apocalypse” can refer to the end of the natural world, but it usually doesn’t — at least, not in the stories we are constantly telling about it. After the world literally ends, there’s not much left to say, is there? In fact, I can only think of two examples off the top of my head of this kind of “last days” story in fiction, when all life ceases to be: On the Beach by Nevil Shute, in which radioactive fallout from a devastating nuclear war kills all animal life on Earth; and Last Night, a film about the Earth’s last six hours before it is destroyed by either a meteor or the sun going supernova (the movie doesn’t specify). In both cases, the story is about how the characters, who know the end is coming, deal with that knowledge and live out their last days. (There is a whole sub-genre of “dying Earth” stories, as well, but these are typically set far in the future and depict a gradual end, rather than an abrupt one.)
More often, apocalyptic stories assume there will be at least a few survivors. The apocalyptic event is not “the end of the world,” as the cliche goes, but rather the collapse of human civilization due to some catastrophe. Those who do survive must start all over again from zero. Usually, this struggle for survival is what the story is actually about, and the apocalypse is just the means to getting there.
We’ve seen these collapses of civilizations in our history. Examples include the Anasazi of the American Southwest, the Indus civilization, the Mayan civilization and the extremely isolated society on Easter Island. This last example serves as a microcosm of societal collapse due to environmental destruction. Over time, the islanders cut down all the trees on Easter Island. This led to soil erosion, making agriculture more difficult, and with no wood, the islanders could not build boats for fishing. The population plummeted: a mini-apocalypse. (For more on this subject, see the book Collapse: How Societies Choose to Fail or Succeed by Jared Diamond.)
In fiction, one of the most memorable portrayals of civilization collapse is in The Mote in God’s Eye, by Larry Niven and Jerry Pournelle. In this case, the civilization is alien, not human. The collapse was always caused by war, brought about by the pressures of overpopulation, and always resulted in total decimation. Survivors rebuilt society, which inevitably led to another collapse. Because the cycle continually repeated itself despite all efforts to prevent it, the aliens became fatalistic and even developed a class of worker whose sole job was to ensure the survival of all knowledge so that civilization could be rebuilt after the next collapse.
The natural world seems to operate on cycles. Day and night, the seasons, the “circle of life,” in which death and decay lead to birth and growth, are all familiar to us. Even the universe itself may be caught in a continual cycle of destruction and rebirth. In human history, we can see how a pattern in how civilizations grow rapidly, reach a zenith, and then either decline or collapse. If an apocalypse does occur, but there are survivors left to start all over again, it seems logical to assume that the cycle would begin again as well, leading to yet another apocalypse. And another. And another. Unless we can find some way to break the cycle, which may mean changing our basic human nature.