The Atlantis Plague is a story about the survival of the human species in the face of extinction. Brought to Earth initially by an alien science ship, the Atlantean ship first arrives when mankind is in its infancy. What later becomes known as the Atlantis Plague is deliberately given to an early example of our species to ensure they would survive an upcoming natural disaster.

Updated over the years by the scientists, this gene therapy advances the human intellect and operates by affecting the way the brain is wired in humans. When another ship arrives, a quiet battle ensues between the Atlanteans in which the scientists are hoping to save mankind while the Atlantean in the second vessel is only interested in building a super army to aid him in his own cause. In a large portion of the population, the brain becomes scrambled and the patients affected seem to devolve, while in a small group of natural survivors, the brain strengthens and they become more intelligent. This group has no desire to find a cure, believing that the plague is meant to be a force of evolution of the human species. Changing people at a genetic level, it seems unstoppable. Over a billion people are infected in the first 24 hours.

One small group of people is determined to stop the progression of the plague, desperately seeking a cure to avoid what is termed the Euthanasia Protocol. Once activated, this would eliminate all of the sick and infected, leaving behind only two groups of people – those who rapidly evolved as a result of infection, and those who devolved. One such group seeking a cure contains Kate Warner, two other scientists, and three soldiers who are inadvertently thrown together, and who stand the best chance of finding a cure. Studying genes in order to find a cure for autism, she has no idea that she is actually one of two Atlanteans who arrived on this planet as evolutionary biologists to study Earth and its inhabitants when Neanderthal still existed. She is even more surprised when memories begin to surface that reveal she is the Atlantean who gave mankind the gene that started it all. Another Atlantean ship arrives years later, carrying a cargo of the only surviving group of their species after their planet was taken by invaders. They don’t agree on the future for mankind.