Dead City follows Molly Bigelow, a seventh-grader at the Metropolitan Institute of Science and Technology (MIST), a science magnet school on Roosevelt Island in New York City. Molly narrates from a bathroom stall at a fencing tournament, sitting beside a zombie she has just killed. She promises to explain how she ended up there, then rewinds to the previous summer.
Molly lives in Queens with her father, a paramedic, and her older sister, Beth. Their mother, Rosemary Collins, a forensic pathologist at the New York City morgue, died of cancer two years earlier. Molly and Rosemary shared heterochromia, each having one blue eye and one green. Rosemary enrolled Molly in Jeet Kune Do, a martial art, and the Junior Birder program, and made her memorize the periodic table during her final hospital stay. Beginning at age seven, Molly spent Fridays at the morgue with her mother, and after Rosemary's death, she continued the tradition with Dr. Hidalgo, Rosemary's best friend.
On the last Friday of summer, Dr. Hidalgo takes Molly and Natalie, his high school intern and fellow MIST student, on a secretive trip to the New York Marble Cemetery, departing without his usual legal pad, staff call, or official van. Outside the locked gate they find a severed finger bearing a wedding ring inscribed to "Cornelius." Molly descends into an underground burial vault and discovers it completely empty, though plaques indicate eight Blackwell family members should be interred there.
When school begins, Molly is isolated after being expelled from a lunch clique the previous year. Natalie sits with her alongside two older students: Alex, a physically imposing and brilliant boy, and Grayson, the school's computer genius. The three seem to be evaluating her.
After school, a grotesque man attacks Molly in the subway station. He sniffs her, rips off a necklace charm she found in her mother's jewelry box, and proves impervious to pain. Natalie arrives, defeats him, and identifies him as a Level 3, the most degraded class of zombie. She squirts vanilla extract up his nostrils to erase Molly's scent and explains the charm is not a horseshoe but an upside-down Omega symbol. The Omegas are a secret network of MIST students who police the undead, and the zombie mistook Molly for a member.
At Grayson's Brooklyn brownstone, the three invite Molly to join their Omega Team. Grayson explains that the undead range from Level 1s, who look and act fully human, to Level 3s, degraded zombies that mostly stay underground. All are confined to Manhattan, sustained by Manhattan schist, dense bedrock found only beneath the island. In 1896, an explosion killed 13 miners digging a subway tunnel and blasted open a pocket of this bedrock, whose energy brought them back as undead. The farther the undead travel from the schist, the weaker they become. Natalie reveals that Rosemary was "the Omega," the most legendary zombie killer in the group's history. Molly accepts the invitation.
Over four weeks, each teammate teaches Molly different skills: history, codes, combat, fencing, and surveillance. Molly realizes her mother secretly prepared her for this life all along; the periodic table serves as the foundation for all Omega codes. For her final exam, the team infiltrates a "flatline party," a social gathering for the undead held in underground tunnels known as Dead City. When a cut on Molly's arm reveals her as living, she fights and kills a Level 3 zombie alone, earning full Omega status.
The team's first assignment from the Prime Omega, the secret leader of all teams, involves three bodies found on Roosevelt Island arranged in an Omega symbol near the historic Blackwell House. Alex spots a woman in a Yankees cap and yellow jacket photographing Molly. Grayson connects the Blackwell House to the empty cemetery vault, and Molly decodes a nearby message spelling "BEWARE."
Molly and Natalie visit the morgue after hours but find the freezer drawers empty. The "corpses" are actually undead, tearing apart Dr. Hidalgo's library for a book. Molly identifies the leader as Cornelius Blackwell by his missing ring finger, chops off his hand with a medical saw to seize the book, and escapes with Natalie to the Alpha Bakery, where a former Omega hides them. Natalie pours triple-strength vanilla concentrate over Molly to mask her scent.
The book is the legendary Book of Secrets, a compendium of Omega intelligence disguised as plays based on Louisa May Alcott's
Little Women. Molly's mother checked it out of the MIST library decades earlier and hid it in the morgue. Dr. Hidalgo retrieves the book and orders the team to forget everything, confirming he is likely the Prime Omega. After he leaves, Molly finds an envelope from the book, labeled in her mother's handwriting with a code translating to "Unlucky 13," the name for the original 13 undead miners. Inside are photographs, including one of the man who chased Molly and her mother onto a rooftop when Molly was five, the traumatic incident behind her lifelong fear of heights.
Driven to investigate, Molly secretly ventures into Dead City. Liberty, a zombie activist and former Omega, reveals the man is Marek, the most powerful of the Unlucky 13, who seeks to eliminate all Omegas. Using Grayson's supercomputer, Zeus, Molly traces Marek to his cover identity as a consultant for the Sandhogs, a labor union of urban miners. She arranges an interview under a fake name, but her teammates arrive, alerted by Zeus's monitoring software. Underground, Marek reveals he recognized Molly by her resemblance to her mother. Grayson saves them with a bluff, threatening to expose Marek's financial crimes. Marek claims he killed Rosemary by forcing dead tissue into an open wound, causing the cancer everyone attributed to an accidental autopsy exposure. He threatens their families.
Natalie takes the team to Dr. Hidalgo, confirming he is the Prime Omega. He suspends the team and removes Molly for her reckless decisions. Natalie invokes her right as captain to appeal, arguing Molly saved the Book of Secrets and is the most gifted Omega they have seen. Dr. Hidalgo accepts the appeal but announces he must step down because his identity is compromised. He formally dissolves the team.
The teammates slowly reconcile, and the narrative returns to the fencing tournament. Molly discovers Marek orchestrated the day: He broke her teammate Hannah Gilbert's arm to get Molly into the competition and sent his own brother, Cornelius Blackwell, to attack her, knowing Molly would kill him. Marek then confronts Molly and demands the Book of Secrets. She uses a fencing fake-out to escape through a window and flees to the George Washington Bridge, riding an elevator up the 65-story tower, gambling that distance from the schist will weaken Marek.
He follows. Atop the tower, paralyzed by her fear of heights, Molly breaks her hand fighting him. The elevator activates again, and the woman in the yellow jacket emerges. She kicks Marek off the ledge into the Hudson River.
The woman kneels beside Molly and lifts her injured hand, brushing the hair from Molly's face. Molly sees eyes identical to her own: one green, one blue. The woman kisses Molly's forehead and staggers to the elevator. As she departs, Molly calls out: "Mom!" The novel ends on the revelation that Molly's mother is undead and has been watching over her.