The Atlantis Gene is a technological/science-fiction thriller published in 2013 by the American author A. G. Riddle. Owing a debt to writers like Dan Brown, Michael Crichton, and Tom Clancy, Riddle constructs a labyrinthine plot involving the lost city of Atlantis, the mysteries of human evolution, and a conspiracy dating back thousands of years. The Atlantis Gene is the first book in The Origin Mystery trilogy, followed by The Atlantis Plague and The Atlantis World. The novel contains depictions of individuals with autism that may be considered marginalizing toward people with neurodivergence.

Plot Summary

When two researchers uncover a Nazi U-boat buried atop a mysterious structure in the Antarctic ice, their discovery triggers a race for the future of humanity. Soon after, two young boys, test subjects in an autism study, are kidnapped from a research facility, and the lead geneticist, Kate Warner, embarks on a dangerous quest to find them. Meanwhile, David Vale, former CIA agent and current Clocktower operative, uncovers a conspiracy to take down the counterterrorism organization, stemming from the Immari corporation, a multinational conglomerate with subsidiaries in both research and private security. When Vale’s investigation connects Immari to the kidnapped boys, he and Warner team up to uncover the reasons behind the kidnapping and to recover the children.

Armed with a series of mysterious, encrypted clues, Vale and Warner are pursued by Immari security forces who force them off the road and kidnap Warner, taking her to an Immari research facility in China. There, Martin Grey, her stepfather and a higher-up in the Immari hierarchy, explains the importance of her research: Brains on the autism spectrum may hold a clue to the long sought-after “Atlantis Gene,” a genetic anomaly that could theoretically determine the future of human evolution. Here, Riddle draws on real evolutionary theory about why Homo Sapiens, of the several hominoid species co-existing 70,000 years ago, survived a mass extinction event when other species, including the stronger, larger-brained Neanderthals, did not. The theory posits that, somehow, Homo Sapiens developed language and tool-building skills in a sudden “Great Leap Forward” which enabled them to develop communal societies. Riddle takes that theory into the realm of fiction by suggesting that an advanced race occupying the city of Atlantis bestowed this genetic gift to humanity, allowing it to survive the “Toba Catastrophe,” the eruption of a supervolcano. Vale sneaks into the research facility and rescues Warner, and they hide out in a safe house while formulating their next course of action.

Both a multinational corporation and a centuries-old secret society, Immari seeks to initiate the Toba Protocol, another mass extinction event which would wipe out all of humanity except for the genetically fittest, who are able to survive the return of the Atlanteans. The Immari research utilizes the deadly effects of the “Bell,” a device found inside both the Antarctic structure as well as a similar structure in Gibraltar, which causes severe internal hemorrhaging and death. The few who survive the Bell will be the forerunners of Immari’s master race.

Warner and Vale split up; Vale will sabotage the facility’s power plant and Warner will find the boys. With the help of a double agent, Warner is reunited with the boys, but the reunion is brief as they are all recaptured. When Dorian Sloane, head of Immari’s Toba Protocol program, places Warner in the Bell test facility, she survives, only to escape shortly thereafter with a wounded Vale amid the chaos of the exploding power plant.

Their escape from the Immari facility leads Vale and Warner to a monastery in Tibet where Vale recovers from his injuries. There, the head of the monastery, Qian, gives Warner a nearly century-old journal. While Vale convalesces, Warner reads the account of Patrick Pierce, a wounded, World War I veteran who falls in love with his caretaker, Helena Barton. When Pierce and Barton become engaged, Pierce is drawn into her father’s web of secrecy. He learns of an excavation below the Bay of Gibraltar which uncovered part of a technologically advanced structure thought to be part of the city of Atlantis. Pierce agrees to lead the excavation team on the condition that he be allowed to marry Helena. But when one of the other team members, Rutger Kane, tries to kill Pierce, he accidentally unleashes the deadly 1918 flu pandemic which kills millions, including the pregnant Helena.

Meanwhile, Sloane has sent armed drones into the mountains of Tibet to search for Vale and Warner. As the drones fire on the monastery, Vale and Warner escape in a hot air balloon and make their way to Gibraltar. When they arrive, Vale guides them to a Clocktower safe house where he, a Clocktower colleague named Keegan, and handful of agents plan a counterstrike against Immari. Keegan, however, reveals himself to be a double agent high up in the Immari hierarchy. He offers Warner a deal: give herself over to Sloane, and he will spare Vale’s life. Soon, she is on a plane to Antarctica where Sloane and a drilling team have discovered an open cavern deep below the ice; it is an opening to the Atlantean structure. There, Sloane reveals his plan to strap two portable nuclear warheads to the boys, send them into the structure—their activated Atlantis Genes will allow them to pass the Bell unharmed—and destroy it, killing the Atlanteans and eliminating the threat.

Back in Gibraltar, Keegan reveals his true identity: Mallory Craig, the Irishman who hired Pierce to lead the excavation team nearly a century before. After the outbreak of the 1918 flu pandemic, Craig, along with Pierce and a young Dieter Kane, was placed in a hibernation tube inside the structure which dramatically slowed the aging process. Having emerged in 1978, Keegan has taken control of Immari. Vale escapes Keegan and flees deeper into the Gibraltar structure where he finds Patrick Pierce, also very much alive after nearly 100 years. Pierce realizes that time inside the structure passes much more slowly than outside, and while he believes he’s been exploring its many chambers for a few months, it’s actually been over 30 years.

In Antarctica, Martin Grey sends Warner down into an ice tunnel after the boys, whom he sent into the structure earlier with the nuclear warheads. But Sloane—now revealed to be an adult Dieter Kane—cuts the cable on the basket, sending her plummeting into the open cavern below. She survives the fall, but her suit is damaged, and she nearly freezes to death before she finally makes her way inside the structure. There, she finds the boys as well as Pierce and Vale who have been transported from Gibraltar to Antarctica via a portal deep in one of the control rooms. Warner and the boys, having been liberated of their deadly packages, escape back to Gibraltar through the portal, followed by Pierce with the two warheads. Sloane and Vale seemingly kill each other in a deadly shoot-out. Martin Grey leads Warner and the boys to a small submarine in which they escape into the Bay of Gibraltar, while Pierce detonates the warheads inside the Gibraltar structure. Warner gazes out at the African coastline, the world now ravaged by a new pandemic. The Toba Protocol is in full effect. As the novel ends, Vale wakes up in a hibernation tube only to see Sloane also preserved within another tube.