Bacon's The New Atlantis can be seen as a melding of two primal ideas that have haunted mankind throughout recorded history. One is the prediction, or the hope, that humanity will advance and create essentially a new world on earth. The other is the belief that at some time in the remote past a civilization existed that was far more advanced than that of the present day and was then destroyed through a natural cataclysm, such as an earthquake or a flood, or through man's own ignorance or mistakes.

In Bacon's story a European expedition comes across an island in the South Seas that has been kept secret from the world and which has developed technological breakthroughs that have made it a paradise in comparison with the known world. Though Bacon's Christian beliefs are made clear (he states that the inhabitants of the island, which is called Bensalem, are Christians themselves), the advanced civilization is a kind of secular version of the perfect world prophesied in Revelation, the final book of the New Testament. Instead of God having created this new paradise on earth, humans have done so. The scientific inventions predicted by Bacon are like a listing of many of the actual creations and discoveries of the four centuries since Bacon's time—medical advances, refrigeration, skyscrapers, the artificial production of "light" (electromagnetic radiation), and the instant transmission of images over long distances, to name the most important and striking ones.

The Atlantis of myth is mentioned by the leader of the Bensalem society. The possibility that such an advanced world existed in the remote past and was then destroyed was first given literary form in Western literature in the Timaeus of Plato. Why does Bacon connect this with his own prophesy of man's ascent? It is likely that is included as a didactic message that whatever man does create is vulnerable, subject to destruction by either natural forces or by man himself. Throughout history, humanity has looked into and speculated about both the past and the future. We have hypothesized about a state of innocence or perfection that was lost and a coming world that either reclaims past glory and peace (a utopia, a kind of heaven on earth) or one in which even the achievements of the present are destroyed—a dystopia, or hell on earth. Bacon presents a utopia but not without the implicit warning that paradise on earth is only a choice for humanity, assuming it is possible. The opposite can just as easily be chosen if mankind allows its imperfections and baser instincts to determine the future.