The Serpentine Army
The Serpentine Army is the result of a fracturing civilization at the height of its considerable powers. The advanced technologies of the planet made it easy to slip away from their humanity, and when their society crumbled, the radicals "assimilated" the rest of the planet and formed themselves into a terrible force called the Serpentine Army. This army is a symbol of the dangers that come with scientific progress; if we're not careful and responsible, we have the potential to lose our humanity and transform into something far darker.
David Vale
David himself is a symbol, which becomes more apparent as the climax of the novel plays out. When the Serpentine Army tries to "assimilate" him, he refuses to submit, stubbornly holding on to his humanity and resisting the overwhelming pull of the assimilation. He finally succeeds in resisting, and his rebellion combines with his DNA to destroy the Serpentine Army from the inside like a virus. He is a symbol for the resilience of humanity and the potential to stand up to the technological loss of humanity by holding fast to its central principles.
The Resurrection Tubes
An avatar from an advanced civilization gives Ares the resurrection tubes, which he incorporates into life on Atlantis. These tubes are symbols for the versatility of scientific advancements: they can be used for either good or evil. The tubes are used in many good ways, like the resurrection of David and the preservation of Kate's child, but they are also used to resurrect evil beings and prolong life beyond its intended capacity.
Ares
Ares is a symbol of utilitarian ethics. He believes that destroying the Serpentine Army is the best course of action for the universe, and he uses this maxim to justify wreaking terrible atrocities on the human race in the name of salvation. This "ends-justify-the-means" system of ethical judgments is proven to be faulty, as Ares essentially kills himself and the army is stopped without the aid of his actions.
Isis
Isis, the Atlantean scientist who saved the human race with the same injected that doomed her own, is a symbolic representation of the potential of well-intentioned actions to go terribly awry. She is crushed with guilt for her inadvertent role in the accidental genocide of her own people, and she tries to make amends by using Kate Warner to defeat the Serpentine Army and restore the balance of the universe. In that sense, she also represents pushing on and continuing to do the right thing despite the possibility of unintended consequences.
