A lot of information points to the story of Atlantis to be based off of the Minoan civilization -a somewhat advanced one at the time- particularly on the city of Akrotiri that had been destroyed by what people have deduced to be a combination of a destructive volcanic eruption followed by powerful waters caused by the tremors of the disaster. Evidence shows that the Minoans did not panic but had very organized and thought-out evacuations. Some information, if I remember correctly, implies that the Greeks finished them off.
Not stating that this is a fact, but a highly supported idea.