The basic theme of Bacon's The New Atlantis is that man is able to advance, to make scientific discoveries that will change and improve his way of living on earth.

In the story a naval expedition comes upon a remote island in the South Pacific which is an analogue to the Atlantis of Western myth that had been given literary treatment in the Timaeus of Plato. The inhabitants of this "new" island called Bensalem have deliberately kept their realm a secret from the rest of the world, though they have made repeated contacts with Europe and other continents by sending out navigators who pose as natives of known parts of the world. Bensalem is a realm of both spiritual and material advancement. Not only is it a peaceful society, it is one in which astonishing scientific breakthroughs have been achieved. Bacon has the leader of Bensalem relate to the European captain a series of achievements which are like a prophesy of what actually has occurred in the modern world in the nearly four hundred years since Bacon's death. He describes buildings the height of skyscrapers, medical advances, refrigeration (that term is actually used by Bacon), the ability to microscopically analyze blood and urine, the ability to generate light artificially, and the ability to transmit images over long distances. All of this is an expression of Bacon's belief in man's ability to improve his world and to use what we now call "the scientific method" to do so.

The fact that he links this with the Atlantis myth is significant. In Plato's telling, Atlantis was an island which existed thousands of years earlier and which held a civilization far more advanced than that of his own time and was destroyed by a great earthquake. Plato's, and by extension Bacon's, theme is a warning that man can achieve things, but that the achievements are vulnerable to destruction, by natural or other causes. In describing a "New Atlantis" Bacon saw into the future and expressed a faith in man's perfectibility, but he also had a darker, more realistic vision of how tenuous our ability to achieve can be in the face of inner and outer dangers.