At the end of the previous novel, The Atlantis Plague, Dr. Kate Warner saved the world by finding a cure for the Atlantis Plague sweeping across the world that included altering a genome in the human body to accommodate both human and Atlantean DNA traces. She also found out that she was actually born in 1918 and suspended in an Atlantean resurrection tube until decades later, and that she has received most of the memories of Isis, the Atlantean scientist who injected humans with the Atlantis gene 70,000 years ago to save humanity. This plot grows in importance in this book, along with everything else - this conclusion just grows everything, especially scope.
Kate is dying from "resurrection sickness," as David finds out near the beginning of the novel, and she has to decide what to do with the last few days of her life. Before she and David can go back and relax in North Carolina, they are visited by Mary Caldwell and her ex-husband, Paul Brenner. Mary has discovered a signal from some extraterrestrial intelligent civilization. Whether this is a good or bad omen remains to be found out.
Meanwhile, Ares (aided by Dorian Sloane) unleashes an enormous flood upon the world by melting the majority of Antarctica, which has long been seen as a center for Atlantean activity. His motivations will be revealed later, but this is the beginning of Dorian's realization that he should probably stop Ares.
Kate realizes that she needs the rest of Isis's memories in order to fully assess and deal with the extraterrestrial situation. Janus apparently took her memories and separated them - some in the Atlantean ship in northern Morocco where Kate and David began the novel, and some in the Atlantean satellite orbiting Earth. To get there, they have to use a particular part in the ship that's guarded by ... invisible flying dinosaurs? They undertake this mission.
Throughout the novel, the story of Atlantis is gradually revealed to Kate and to the readers, and here seems like an appropriate spot to pause and relate the story in its summarized entirety. A really long time ago, the pre-Atlanteans (headed by Ares, their war general) discovered a super-powerful civilization in space, and when they went to investigate, they found a battle of small ships fighting what seems to be a giant mechanical serpent (the Serpentine Army), which "assimilates" new beings into itself and continues to grow stronger. Ares captures some of the civilization's advanced defense drones and acquires the resurrection tube technology, then escapes and founds a new civilization, Atlantis. He programmed these drones to attack and destroy any intelligent beings who were not Atlantean (recognized by scanning the being's biology). Meanwhile, Isis, a kindhearted scientist, has been experimenting with gene therapy (the beginning of the Atlantis gene), and she injects several people in Atlantis with the gene. When she and Janus are away on a scientific expedition - the one where they save the human race - Ares's drones become unable to recognize the Atlanteans because of their altered biology due to Isis's gene therapy, and they open fire, destroying the Atlantean home world. Isis is therefore inadvertently responsible for the near-genocide of her own race. Ares enacts his revenge, attacking the ship of Janus and Isis and putting them out of commission for quite a while.
The only way to defeat the Serpentine Army is to resist its overwhelming "assimilation," requiring a person of immense willpower and conscious desire to fight back. If this rebellion is successful, the person's DNA will act as a virus and break the army apart from the inside. Ares unleashes the flood on Earth in order to try to create a human with such legendary resilience; ironically, that human already exists, and Ares is trying to kill him.
While on the Atlantean satellite, David is blown out into space by a grenade, where he is picked up by the Serpentine Army, and they try to assimilate him into the great mind. David, unreasonably stubborn human that he is, refuses to cooperate, and his rebellious human DNA corrupts the Serpentine Army, rendering it powerless.
At the same time, Dorian has rebelled against Ares, killing him over and over as they are both continually reborn into resurrection tubes. In the process, Ares explains his strategy, and just before Dorian kills him for the last time, Ares disables his resurrection setting, and he never comes back. Dorian, knowing that he has triumphed over his foe and done humanity a favor, turns off his own resurrection and ejects himself into space, dying almost instantly.
In the end, humanity is saved from the multitude of threats from the Atlanteans, the Serpentine Army, the plague, and the Immari, and David and Kate settle down to raise a family.
