The novel is set more than 150 years in the future. Scientists used DNA technology to bring dinosaurs back from extinction, but the creatures carried ancient bacteria and viruses that triggered the Dinosauria Pandemic, killing victims in hours and wiping out nearly all of humanity. A leader who called himself the Noah rallied immune survivors into four underground nuclear bunkers, and dinosaurs reclaimed the surface. Generations later, the remaining humans live in these cramped compounds, governed by strict rules of shared labor, pledging obedience to the Noah's authority.
Eleven-year-old Sky Mundy lives in North Compound, where she is a social outcast. Five years earlier, her father, Jack Mundy, one of the compound's top scientists and technology specialists, vanished. A mandatory assembly declared him a traitor who stole vital supplies, and residents turned their resentment on his daughter. Sky was sent to the Guardian Wing, housing for people without families, where General Ron Kennedy, the compound's head marine, locked her in a stone room. That first night, Shawn Reilly, orphaned when his parents died in a tunnel collapse, picked her lock and introduced himself. Shawn became her closest friend, eventually moving in with his aunt, a council member, yet still sharing food with Sky and helping search for information about her father.
Convinced Jack left for a reason, Sky risks her life sneaking topside to intercept the quarterly maildrop, copying data from the marines' information boxes in hopes of finding clues. On her twelfth birthday, Shawn reveals a discovery: While trying to fix her father's broken compass, he found a hidden compartment containing a note and a map. The note, in Jack's handwriting, explains that he belonged to a secret group called the Colombe, students who believed humans and dinosaurs could coexist. He stole critical information stored on a data plug inside the compass and asks Sky to deliver it to another Colombe member: either a man named Ivan or a contact at a marked point in the middle of Lake Michigan. That same day, a council member announces the Noah's decree to install locks on all exit hatches within twenty-four hours, and Sky resolves to leave immediately.
At four in the morning, Sky sneaks out and infiltrates the marines' barracks during a shift change, stealing rope, a canteen, and rations. She holds her father's data plug up to the marines' port screens, data-reading devices, to check compatibility, not noticing a security camera recording her. The compound alarm sounds early. Sky races for the exit but finds the electrified emergency gate has dropped. Shawn appears, hacks the control panel to deactivate the gate for thirty seconds, and shoves her through. He gets stuck halfway, and Sky hauls him free just before the gate reactivates. They escape through the hatch and padlock it shut. Marines who exit through a different hatch are attacked by deinonychus, predatory dinosaurs, and one marine loses part of his leg, a consequence that weighs on Sky.
Shawn reveals he planned to come all along, bringing his own stolen camouflage body-armor suit and a stun gun. They plunge into dense forest, struggling with blistered feet, humid air, and sensory overload. Sky feeds a small dinosaur she names Herman, and it follows them. When a Tyrannosaurus rex appears in an open meadow, Sky pulls Shawn flat and their camouflage suits conceal them. Herman darts toward the predator, and they sprint to the trees.
A boy named Todd Birch, roughly their age and raised entirely aboveground, grabs Sky's shoulder. He disassembles Shawn's stun gun in seconds, revealing it is a nonfunctional shell, and explains that Herman is actually Verde, his trained pet dinosaur, which Todd sent to distract the T. rex. Todd brings them to the Oaks, a hidden village of about thirty people living in tree houses built on dinosaur-bone frames. The village leader, Jett, searches them for tracking devices and allows them to stay. A mapmaker named Roderick marks Sky's map with safe routes. At a trading post, they trade their body armor and Shawn's music box, his last keepsake from his dead mother, for bows, arrows, knives, and boots.
Three Noah helicopters appear. Marines led by General Kennedy capture the villagers at gunpoint. Kennedy grabs Todd's mother, Emily Birch, and threatens to kill the women unless everyone surrenders. Sky tackles Todd before he can charge into the open and reveal their position. Roderick tries to flee and is shot dead. Kennedy interrogates Jett and Emily about Sky and Shawn; both deny seeing compound children. The village is loaded into helicopters and flown away. Sky, Shawn, and Todd watch from the bushes in helpless horror, realizing the marines tracked them to the Oaks.
Todd turns on Sky with his bow drawn, blaming them for the attack. They find no tracker and conclude the marines want the data plug, which Sky inadvertently revealed on the barracks security camera. Todd agrees to guide them to Lake Michigan in exchange for their promise to help rescue the villagers. He reveals he knows a dinosaur hunter named Ivan, the same name from the note. They swap all compound-origin gear for new supplies to eliminate hidden trackers.
The trio pushes north through dangerous terrain. Todd teaches them archery and survival, and they sleep in tree pods, canvas hammocks hung high in the trees to avoid nocturnal predators. Sky kills a massive spinosaurus with an arrow through the eye when it attacks their tree at dawn. Later, a pack of scavenger dinosaurs pursues them until arrows rain from above, killing several. The shooter is Ivan, a wiry old man missing part of his right arm, which he has replaced with a leather-and-metal bow brace. Ivan leads them to his home atop an abandoned skyscraper.
Ivan reveals that Sky looks exactly like her mother, Clara, who was Ivan's daughter. Ivan is Sky's grandfather. Clara grew up topside but wanted a formal education, so Ivan helped her infiltrate East Compound's university. There she met Jack Mundy, and together with other students they formed the Colombe, named for the French and Italian word for "dove," referencing the biblical dove that told Noah it was safe to leave the ark. The Noah discovered the group and scattered its members across the compounds. Clara tried to escape and was killed; Jack told Sky her mother died in childbirth to protect her from this truth. Ivan's device for reading the data plug was destroyed two years ago, so the mission must continue to Lake Michigan.
After training the children in archery, Ivan gives Todd a new bow crafted from the same dinosaur as Todd's late father's original weapon. Marines ambush them, and Ivan orders the children to flee while he fights. General Kennedy intercepts them in the woods, holding Shawn at gunpoint. Kennedy reveals that Jack was implanted with a tracker, captured, and killed within a day of leaving the compound. The marines recovered a plug from his body but did not know a second copy existed until Sky appeared on the security camera. Sky charges Kennedy and slashes his face, drawing blood that attracts saltopus, small scavenger dinosaurs. Todd and Shawn overpower two other marines, and all three children escape while the creatures swarm Kennedy.
That evening in the trees, Sky processes what she has learned: Her mother was murdered, her father was killed delivering the same plug she carries, and the Noah has sanctioned violence against his own people. Shawn, who believed deeply in the compound system, struggles with the collapse of his worldview. Sky resolves to complete her father's mission, help Todd rescue the Oaks villagers, and build a new life on the surface. She watches a distant brontosaurus herd cross a meadow in the fading light before climbing into her tree pod, ready for whatever comes next.