On its surface, The Atlantis Gene: Book I is a science-fiction novel about good and evil. But, it's more than that in its design. The novel contains wild conspiracy theories about the Nazi regime in WWII, 9/11, aliens, subterranean lifeforms—but all of those pale in comparison to the novel's central idea: Alien lifeforms spliced pre-human DNA to create human consciousness, and there are latent portions of the human genome that, when activated, return alien powers to the humans. This idea is very close to spiritual transcendentalism, so one interesting way to interpret the plot is as a spiritualist narrative about the progress toward "enlightenment" which the novel calls "gene activation."
As David and Kate progress together in their joint hero's journey, they learn more about the world's secrets. They learn that the Immari people want to destroy the superhuman Atlanteans, and they will stop at nothing to succeed in world domination. The heroes realize through this that their battle is not against actual villains, but the force of evil itself. The Immari merely symbolizes the ancient dilemma between right and wrong, good and evil. Notice also that the Immari operates as if their interests are ethical and obvious, but their methods reveal their true intent.
By the end of the novel, we're all set up for a sequel. The issues of the first novel are considerable: Science, philosophy, WWII history, current events, religious transcendentalism, genetics, et al. By the end, the problem has become much more severe, and although David was roped into the story as a mercenary job, he has become twisted up in the plot so much that it's now his story as well, not just the geneticist.