In entries in her "gleaning journal," Scythe Curie gives the reader the history of her world. in 2042, humans became immortal and created the Scythedom, an organization of scythes—people trained to "glean," or kill others permanently—to control the population growth. This job is the only one not overseen by the Thunderhead, an advanced version of "the cloud" that has replaced government and oversees every aspect of the population. With immortality has come the sense that there's no longer a point to life, and people in Curie's age don't understand what it was like to live knowing that death was inevitable.
Seventeen-year-old Citra is horrified when Scythe Faraday shows up on her family's doorstep and invites himself for dinner. She and her parents are terrified that he's going to glean them, and Citra angrily snaps at him. He admits he's here to glean their neighbor. Not long after, Faraday shows up at Rowan's school to glean the quarterback, Kohl Whitlock. Rowan stubbornly insists on holding Kohl's hand when Faraday electrocutes him, and for this, Rowan's classmates, including his best friend Tyger, shun him. When Faraday invites both Citra and Rowan to become his apprentices, they both accept; however, only one of them will become a scythe.
Faraday believes in using accidental death statistics from the Age of Mortality to choose his victims. For instance, he chooses to glean a heroic dog lover because many people used to die saving their pets from raging rivers. One of Faraday’s other quirks is that he insists on attending every funeral for the people they glean. And although Faraday takes his vows as a scythe very seriously, he doesn’t always follow the rules: once, when a man fights back—which, by law, means that Faraday must kill his whole family—Faraday instead grants the man's wife and children immunity, aweing Citra. Under Faraday’s direction, Citra and Rowan grow strong as they study "killcraft," as well as science and the humanities. They learn Black Widow Bokator, a martial art, and as time goes on, Rowan and Citra develop crushes on one another but do their best to ignore those feelings, as scythes are not allowed to fall in love or have families.
Elsewhere, Scythe Goddard and his followers, Scythes Rand, Volta, and Chomsky, conduct a mass gleaning on an airplane and then in the food court of a mall. They're both bloody and fiery affairs, as Chomsky loves using a flamethrower. At the mall gleaning, the bloodthirsty Goddard uncharacteristically spares a ten-year-old girl, Esme, and takes her home with him. He lives in a mansion that he took over from a terrified business executive, Maxim Easley, who is now forced to work as Goddard's pool boy.
In May, Vernal Conclave arrives. Conclaves take place three times per year, and it's the only time that the Scythedom performs oversight functions on itself. Apprentices also undergo testing at these events, and new scythes receive their rings. Citra is concerned when she learns that the High Blade of MidMerica, Xenocrates, didn't know that Faraday took two apprentices, which is an unusual practice. At conclave, Citra and Rowan recognize Goddard—decked in diamond-encrusted robes—and make note of Faraday's clear distaste for him. The morning's proceedings are ceremonial and bore Citra. In the evening, Scythe Curie tests the apprentices with questions designed to gauge their morality and their knowledge. Citra fails her test by lying about the worst thing she's ever done, while Rowan fails on purpose to make her feel better. At the very end of conclave, Scythe Rand puts forward the motion that at the end of Citra and Rowan's training, whichever apprentice becomes a scythe should glean the other. Xenocrates lets it pass.
The morning after conclave, still reeling from this news, Faraday tells Rowan and Citra that nothing will change and goes out alone. Rowan and Citra kiss while he's gone, hoping to get it out of their systems. That night, they wake up to two BladeGuard officers and Xenocrates on Faraday's doorstep—Faraday self-gleaned (killed himself), which frees them from their apprenticeships and means they won't have to glean each other. However, Scythe Goddard has offered to take over Rowan's training, while Scythe Curie will train Citra, so Faraday’s sacrifice was futile. Citra is suspicious of Curie, as Curie lives in a grand house and cooks food for her (apprentices are supposed to cook for their mentors). The next morning, Curie takes Citra gleaning and stabs a man, suddenly and without warning, whom she insists was "stagnant." Later, Curie invites the man's family to her home for dinner to grant them immunity and to share in their grief. Citra begins to trust Curie and confides in her the actual worst thing she's ever done: as a child, she pushed a classmate in front of a truck. Curie makes Citra find the classmate, Rhonda Flowers, apologize, and allow Rhonda to push her in front of a truck. Rhonda refuses, which makes Citra feel silly. When Curie points out that the Thunderhead certainly saw Citra push Rhonda because it sees everything, Citra starts to wonder if someone murdered Faraday and if the Thunderhead saw it happen.
Rowan decides to let Citra win the scythehood. He arrives at Goddard's mansion in the middle of a fantastic party in his honor. Goddard insists that the home and the party supplies were donated—scythes aren’t allowed to own much—and says that he believes scythes should enjoy life. Rowan notices Esme and comments on her, but Goddard says that Esme is the most important person at the party. The party continues for another day. When it finally ends, Volta takes Rowan to a wine cellar. Goddard and his crew turn off Rowan's pain and healing nanites, which allow him to heal quickly and not feel pain, and beat him to a pulp. Volta, Esme, and then Goddard visit Rowan. Goddard insists that in order to have a clear mind, Rowan must feel pain. Rowan begins training daily on dummies and feels himself turning into a soulless "killing machine." Goddard encourages Rowan to enjoy killing. The only person that Rowan thinks doesn't truly believe in Goddard is Volta, though Volta stands by the first time that Goddard forces Rowan to practice gleaning on live subjects. Rowan feels disgusted with himself.
One afternoon, as Citra tries to track down the family of one of Curie's gleaning victims, she finds herself in a Tonist cloister in pursuit of a Tonist named Brother Ferguson. He refuses to attend to his sister's body or funeral, and explains that the Tonists don't believe that death by a scythe is a real death. Citra is especially incensed when, after she hits the "bident," a massive tuning fork that makes "the sound of the universe," Brother Ferguson argues that Tonism keeps people from getting “stagnant.” Citra begins spending time searching for evidence of Faraday in the Thunderhead's "backbrain." She finds compelling information only after using some of her own photographs from the area where Faraday died to piece together evidence to support her suspicions.
Goddard announces that it's time to take Rowan to one of his mass gleanings, this time at Magnetic Propulsion Laboratories. Goddard and his crew take a helicopter to the building, land on top, and systematically kill everyone they can in the building. Rowan does his best to point people to unguarded exits. When Goddard announces they're finished, he points out to Rowan that the firefighters cannot put out the fire from Chomsky's flamethrower since it's scythe activity. He allows Rowan to wear his ring to grant survivors immunity. He throws a feast that night, but Rowan excuses himself to play cards with Esme. Rowan later discovers Volta crying in his bedroom. Though Volta knows that Goddard is evil, he doesn't believe it's possible to escape him now.
At Harvest Conclave, Citra is angry to see Rowan surrounded by adoring apprentices. When they finally have a moment to speak, she quietly fills him in on her research and her suspicion that Goddard killed Faraday. The test for the apprentices is a Bokator match. Both Rowan and Citra fight in such a way as to try to let the other win, but Rowan realizes that in order to allow Citra to win the scythehood, he needs to do something drastic. He snaps her neck, rendering her deadish for several days.
Goddard throws another lavish party. Volta overhears Xenocrates and Goddard talking about getting rid of "the girl," and perplexingly, Goddard forces Xenocrates to jump in the pool by putting a knife to Esme's neck. After the party, Rowan confronts Goddard about this and about Citra's suspicion that he killed Faraday. Goddard denies it, and later Volta lets Rowan in on what he discovered: Esme is Xenocrates's illegitimate and illegal daughter, so Xenocrates will do whatever Goddard wants to keep her existence a secret.
Citra finally admits to Curie that she believes Faraday was murdered and that she told Rowan of her suspicions. Curie encourages Citra to stop researching and dedicate herself to winning the scythehood so she can fight the corruption from the inside. That afternoon, while Citra is home alone, two BladeGuard officers arrest Citra and take her to Xenocrates. He and Scythe Mandela accuse her of killing Faraday and to prove it, he shows her one of Faraday's journal entries saying that he's afraid his female apprentice is going to kill him. Citra pushes past Faraday and throws herself off of Xenocrates's building, rendering herself "deadish." While she's dead, the Thunderhead speaks to her, says it's concerned for the fate of the Scythedom, and gives her a clue: the name Gerald Van Der Gans. Four days later, Citra wakes up in the Chileargentine region with Curie. Curie explains that someone tried to frame Citra, and the journal entry was actually about Curie herself more than a century ago: Faraday was Curie's mentor, and, later, her lover. She gives Citra Tonist robes and sends her north to Amazonia. Citra believes she's after Faraday's killer, Gerald Van Der Gans, but when she arrives at her destination, she discovers Faraday himself—Gerald was his childhood name, and Curie is the only one who knows he's hiding in retirement. He reassumes Citra’s training.
A few days before Winter Conclave, Citra flies home, cleared of all charges, and Goddard takes his crew on a gleaning rampage at a Tonist cloister. It's a bloody and awful affair, and after gleaning a room full of children and experiencing a moral crisis, Volta weeps and self-gleans. Rowan kills Goddard, Chomsky, and Rand, burns the building down, and pretends to be a scythe to get the firefighters to leave it alone. Two days later, Xenocrates meets with Rowan and attempts to blame the tragedy on Rowan until Rowan lets on that he knows about Esme. The next day, both Rowan and Citra take their final test. Citra is distraught to realize that she must render her little brother Ben deadish in front of a panel, but she does it compassionately. The next day at conclave, the Scythedom bans gleaning using fire, and then Citra earns her scythe's ring instead of Rowan. She insists on taking the name Anastasia Romanov, which she says represents the potential for a better future. Just as she turns to glean Rowan, she punches him in the face with her ring, giving him immunity. She sends him out to a car waiting outside, and Rowan is shocked to find Faraday driving. In an entry to her gleaning journal, Citra writes that she's heard rumors of a rogue, unordained scythe called Scythe Lucifer taking out corrupt scythes with fire.