At the Los Angeles Zoo, a female lion named Mosa and a dominant male named Dominick have grown increasingly tense and silent over recent weeks. When assistant zookeeper Terrence Larson enters the enclosure to deliver food, the lions coordinate an ambush and kill him. They escape through the open gate, flee into Griffith Park where Dominick kills a golfer, and run toward the city, drawn by the pervasive scent of humans.
In Harlem, Jackson Oz, a dropout from Columbia University's PhD program, monitors television screens tracking what he calls Human-Animal Conflict (HAC). His data show that the worldwide rate of wild animal attacks over the past four years is double the average of the previous 50, with domestic animal injuries spiking in Australia, Beijing, and Britain. He has maxed out his credit cards and was laughed off the stage at a Paris animal rights conference trying to spread his message. Oz lives with Attila, a five-year-old chimpanzee he rescued from a New Jersey biomedical lab where the animal had been subjected to olfactory experiments. Attila has post-traumatic stress disorder and communicates using a Picture Exchange Communication System (PECS), a talking touch-screen device.
After the LA attacks, Oz receives a text from Abraham Bindix, an Afrikaner safari guide, who reports that lions slaughtered an entire village near Zimbabwe and urges Oz to come to Botswana with cameras. Oz's girlfriend, Natalie Shaw, a Columbia medical student frustrated with his obsession, reluctantly agrees to care for Attila while he is away. They strike a deal: If the trip fails, Oz will abandon his crusade. During the flight, Natalie emails to break up with him and renege on her promise.
In Botswana, Oz and Abe fly to Abe's brother Phillip's game lodge in the Okavango Delta, which they find deserted. Two safari groups totaling 20 people have been missing for two days. They discover an abandoned vehicle surrounded by blood-stiffened clothing. Approximately two dozen male lions surround the truck in coordinated formation, an impossibility in known lion behavior since males never congregate in large groups. A charging lion knocks Abe from the vehicle, and Abe dies when Oz crashes the truck off a riverbank. Stranded, Oz recovers his camcorder, which captured footage of the aberrant behavior.
Following the river, Oz rescues Chloe Tousignant, a population ecologist from the École Polytechnique in Paris, who is clinging to a rock surrounded by Nile crocodiles. Her research team was ambushed by lions days earlier. A bush pilot rescues them and warns that the Botswanan government will suppress the footage to protect tourism. Oz hides the tape on his body and convinces Chloe to accompany him to the US, arguing her credentials will lend credibility to his findings.
Meanwhile, Natalie visits Oz's apartment to check on Attila despite the breakup. In chapters told from Attila's perspective, the chimp is disturbed by a pervasive "Bad Smell," the scent of humans, which triggers uncontrollable rage. He ransacks the apartment and terrorizes a neighbor.
In Washington, D.C., former Columbia professor Gail Quinn has arranged for Oz to speak at a Senate hearing, but a senator's staffer cancels the appearance, dismissing his theory as fringe. Oz climbs a sculpture in the Senate atrium to shout his warning, and Capitol police arrest him along with Chloe and several allied scientists. Back in New York, Oz and Chloe arrive at his apartment to find it destroyed. Attila, wearing Oz's red hat, attacks Oz and flees out the window. In the back bedroom, Oz discovers Natalie's decomposing, partially eaten body, identifiable by her red hair and hospital ID badge. Attila killed her, and Oz is consumed with guilt.
Five years pass. Oz has married Chloe, and they have a three-year-old son named Eli. Oz has written a controversial bestselling book about HAC, and Harvard biologist Harvey Saltonstall serves as his most prominent public critic. His Columbia team has found that aggressive animals show abnormal brain growth concentrated in the amygdala, the region governing memory, learning, and smell, but cannot identify the cause. The government secretly summons Oz to a National Security Agency (NSA) facility, where officials reveal HAC has arrived in the US as a full-blown crisis. They show footage of a massive pack of dogs running along a California highway and designate the crisis "ZOO," noting that all attacking animals are male. General Albert Garcia advocates military extermination, but Oz argues for research and is overruled.
Following a stray dog through Manhattan, Oz crawls into a vast underground chamber beneath Bryant Park where thousands of dogs behave like social insects. He realizes the crisis is pheromonal, not viral: Hydrocarbons, the building blocks of both pheromones and petroleum products, have been altered by electromagnetic radiation from cell phones, creating a substance animals interpret as an attack pheromone. Humans are unaffected because they lack a functional vomeronasal organ, the nasal tissue that detects airborne pheromones. NYU biochemist Dr. Mark Valery confirms the theory and discovers that human sebum, the oily substance on skin, now contains compounds resembling insect attack pheromones. Animals attack because humans smell like a threat.
At the White House, Oz learns that the president's daughter was killed by the family dog. Grief-stricken, President Hardinson has authorized napalm strikes on animal nesting sites, but the bombing campaigns prove ineffective. When Oz's vehicle is attacked and he is trapped in the wreck, he drives off an approaching grizzly bear with a smoke grenade, realizing that smoke disperses the pheromone signal just as beekeepers use smoke to neutralize bee pheromones.
Back at the government safe house on Manhattan's Upper East Side, a soldier accidentally leaves the electric fence gate open. Attila, still wearing his ragged red hat, leads a horde of dogs, rats, cats, and raccoons through the breach. He and two other chimps climb to Chloe and Eli's balcony and begin smashing the glass doors. Chloe shields Eli with her body. At the threshold, Attila catches a scent from the child that triggers a buried memory of Oz rescuing him from his cage. He shrieks a warning, prevents the other chimps from entering, and leads them away.
At the White House, with world leaders videoconferenced in, Oz proposes the only solution: Cease all cell phone use, electricity, and fossil fuel burning worldwide for at least two weeks to clear the air. President Hardinson announces emergency executive orders, and major nations agree. The shutdown, called "the Big Stop," causes animal attacks to plummet from thousands per day to three. But the Big Stop collapses after only three days as governments and citizens resume using electricity and cell phones. Petrochemicals and electromagnetic radiation flood back into the environment, and animal aggression resumes worse than before.
The White House is overrun by animal hordes and the Capitol building catches fire. Oz demands that his family be included on the evacuation flight to Thule Air Base in northern Greenland, where extreme cold and the absence of mammals make it safe to use generators. During the flight, the plane strikes a massive swarm of bats and loses an engine before making an emergency landing. The family eventually reaches Greenland. In the epilogue, Oz writes from an arctic bunker in near-constant darkness. He reflects on a recurring dream of an ant death spiral he once witnessed in Costa Rica, thousands of ants blindly chasing each other in an endless circle until they die, which he sees as a metaphor for humanity's self-destructive path. Despite everything, Oz expresses hope that human resilience will prevail, drawing strength from watching Eli, then immediately questions his own conviction, ending the narrative on a note of deep uncertainty.