The one guess (it does not qualify as a theory) that makes the most sense about the Atlantis Myth is that Plato made it all up in an attempt to illustrate the concept of hubris.
The only other guess is that the Atlantis Myth is derived from oral histories dating back to the end of the most recent glaciation period. That is, as the "Ice Age" came to an end, the massive ice sheets covering most of North America, Asia, and Europe melted, filling the oceans, and causing the sea level to rise. All of the villages and settlements that were once well above sea level were slowly inundated and covered by the rising waters. Even though this process may have taken 400 years, the subsequent 300-foot rise in sea level was remarkable enough that every culture from all over the world had a story about how their ancestral towns were swallowed by the sea. After many tellings, exaggeration was bound to take hold -- what was originally an 8-inch rise in sea level every year that eventually swallowed the local fishing village became the overnight sinking of an entire continent into some far-off ocean. Human nature being what it is, this exaggeration eventually became accepted as 'truth' to people for whom the word 'science' has more to do with superstitious nonsense than with methodical evidence-gathering.
What we know as the 'Atlantis Myth' is nothing more than an oft-repeated story told of ordinary events that happened 12,000 to 15,000 years ago -- roughly 6500 to 9500 years before the first known written language!
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The mere fact that science may not yet adequately explain an object, event, or experience does not mean the immediate explanation should automatically default to a conspiratorial, extraterrestrial, paranormal, or supernatural cause.