The novel opens with FBI Special Agent Atlee Pine visiting ADX Florence, a federal supermax prison in Colorado, at midnight. Pine, 35 and assigned to a one-agent resident agency in Shattered Rock, Arizona, near the Grand Canyon, confronts Daniel James Tor, a serial killer serving nearly 40 consecutive life terms. Pine believes Tor entered her family's home in Andersonville, Georgia, on June 7, 1989, when she and her twin sister Mercy were six years old. The intruder used a nursery rhyme to choose between the twins, thumping each girl's forehead with each word. Mercy was taken; Pine was left with a cracked skull. Tor refuses to confirm or deny involvement, instead probing Pine psychologically until she involuntarily touches her FBI badge for comfort. Reading this as weakness, he ends the meeting, telling Pine he has "defined your entire, pathetic life."
After Mercy's disappearance, Pine's parents divorced, each blaming the other for being too intoxicated to hear the intruder. Her father later killed himself on the twins' birthday. Pine grew aimless until a fortune teller at a county fair sensed "two pulses, two hearts" but "only one soul," galvanizing Pine to live for both herself and her sister. She became a star athlete, narrowly missed the U.S. Olympic weightlifting team, and joined the FBI. Six months before the novel begins, hypnosis sessions produced Tor's image from Pine's subconscious, though she cannot be certain the memory is genuine.
Halfway back from Colorado, Pine is summoned to the Grand Canyon, where a mule named Sallie Belle has been gutted with a knife and its rider is missing. The rider registered as Benjamin Priest, a DC employee of a company called Capricorn Consultants. Pine finds evidence the carcass was moved and discovers the letters "j" and "k" carved into the hide. At her office, Pine's secretary Carol Blum, a sharp Bureau veteran, connects the letters to a 1909 legend about explorers named Jordan and Kinkaid who allegedly found a hidden cave in the Grand Canyon. Pine learns Capricorn Consultants does not exist and is alarmed to find senior National Security Branch officials monitoring the case. Her office computers have been hacked.
A photo from Ed Priest, Benjamin's brother, reveals that the man who rode the mule was an imposter. Pine has a sketch produced of the imposter's face. Ed flies to Arizona carrying a concealed pistol. Pine, suspecting danger, sets a decoy in her bed. That night, Ed approaches with his gun but cannot pull the trigger. He confesses that unknown callers threatened to kill his family unless he murdered Pine. She records his confession, arranges protective custody for his family, and forces Ed to contact his brother. Ben agrees to meet at El Tovar Hotel on the South Rim.
Ben arrives disguised as a woman and admits he formerly worked in intelligence but refuses to reveal details. As they drive south, their vehicle is rammed from behind. The gas tank cracks and flames erupt. Concussed, Pine is roused by a vision of young Mercy calling, "Hurry, Lee. Come on. You're in trouble." She pulls both brothers from the burning vehicle before a military helicopter lands and soldiers throw a flashbang grenade, knocking her unconscious. She awakens in a hospital; both brothers have been taken and the crash site meticulously cleaned.
Clint Dobbs, the Special Agent in Charge at the Phoenix Field Office, orders Pine off the case. Instead, Pine and Blum go rogue, sending decoys in opposite directions while slipping out at midnight in Pine's 1967 Ford Mustang with only cash and burner phones for the 2,200-mile drive to Washington, DC.
In Old Town Alexandria, Pine breaks into Ben's empty house and discovers a flash drive hidden inside a partially deflated basketball. Two men with Russian-made pistols attack her; she knocks both unconscious. Outside, a small Asian man of extraordinary martial arts skill ambushes her, nearly defeating her before a police siren forces his retreat. Pine then connects with Simon Russell, an associate of Priest from a church basketball league. Russell reveals that Priest worked for the CIA and then Defense Intelligence before going independent, and he mentions the Society for Good (SFG), a prestigious think tank where Priest is a member. Before Russell can say more, the Asian fighter kills him with a single fatal kick. At SFG headquarters, a member named Phillip identifies the attacker as Sung Nam Chung, a South Korean-born freelance operative.
Pine cracks the flash drive's password by combining zodiac references to Capricorn with the names of Ed Priest's sons. The drive contains technical diagrams with Korean characters referencing fissile material and a map pinpointing coordinates in the Grand Canyon. Oscar Fabrikant, SFG's longtime senior figure, flies to Moscow to investigate Russian involvement and is found dead, ruled a suicide Pine knows was murder.
On the train back to Arizona, Chung boards after tampering with signals and captures Blum at gunpoint, demanding the location of David Roth, the man who impersonated Priest on the mule ride. Pine attacks with a metal pipe and forces Chung out a broken window in a desperate struggle. Chung is killed.
Pine descends into the Canyon alone at midnight. Over three nights, she avoids armed soldiers and overhead helicopters. On her last night before supplies run out, she locates a camouflaged cave. The soldiers corner her at gunpoint, but Sam Kettler, a park ranger and ex-Special Forces veteran who had been independently tracking the helicopter activity, shoots two of them. Pine kills the third.
Inside the cave, David Roth reveals the conspiracy. A tactical nuclear weapon with Korean markings was supplied by Russia using recycled North Korean materials and placed in the Canyon by elements within the U.S. government. The plan was to "discover" it publicly, blame North Korea, and fabricate justification for war. The device was deliberately built without key components so it could never detonate, but this detail would be concealed from the public. Roth learned of the plot from Fred Wormsley, a high-ranking National Security Agency (NSA) official who was recruited for the mission, secretly opposed it, and was subsequently murdered. Pine identifies concealed Russian surveillance cameras embedded in the weapon, proving Moscow's real objective: recording American officials planting the bomb to create permanent blackmail leverage over the United States.
Pine, Kettler, and Roth carry the nuke out on a grueling overnight climb, surviving Roth's near-fatal fall and a helicopter searchlight pass. They transport the device to the Tuba City police station on sovereign Navajo land and then secretly to Pine's office in Shattered Rock.
When Dobbs arrives with agents, armored soldiers storm the office demanding Pine and Blum for treason. Dobbs refuses to surrender them. Pine reveals the nuclear weapon, and the leader's recognition of it as a nuke before being told exposes his involvement in the conspiracy. She produces the Russian surveillance devices and discloses that a hidden camera has recorded the entire confrontation, with footage already uploaded to a secure cloud. Pine leverages this evidence to secure the Priest brothers' safe return, compensation for victims' families, and assurances against retaliation. The conspirators remove the weapon and depart.
In the aftermath, waves of high-level government resignations sweep Washington and peace talks with North Korea restart. Pine visits the recovering Priest brothers, declines a prestigious government posting, and returns to Shattered Rock. She drives her Mustang back to ADX Florence, arriving just before midnight, places an old Polaroid of herself and Mercy against the glass, and asks Tor, "Where's my sister?"