Citra and Rowan, two MidMerican teenagers, separately encounter a state-sanctioned killer known as a scythe. In their society, a future America in which a computer system named the Thunderhead controls most aspects of life and natural death no longer exists, the only form of death that remains comes at the hands of scythes, who select people for execution in an act called gleaning. Citra’s family unexpectedly hosts a scythe for dinner before he gleans their neighbor, and Rowan meets the same scythe as he consoles a classmate targeted for gleaning. Soon, both teenagers receive a mysterious invitation to the opera, where they realize that their invitations have come from the scythe they met previously, Scythe Faraday. Faraday offers them a trial apprenticeship that will last for a year, after which Faraday will choose one of them to become his formal apprentice. Citra and Rowan both protest that they do not want any part in Faraday’s grim world. But Faraday insists that their objection only confirms they are fit to become scythes, since good scythes are not eager to kill.  

Citra and Rowan train as apprentices while living in Faraday’s home. Though the work is physically and emotionally draining, Citra and Rowan find the more idealistic side of scything rewarding. They also develop an attraction to each other that they do not act on because Faraday has forbidden romance between them. Citra and Rowan witness a darker side of scything at a Conclave, a regular regional gathering for scythes held a few times a year. They meet one of the more controversial scythes, Goddard, who is notorious for conducting mass gleanings. While at the Conclave, Citra and Rowan take an apprenticeship test administered by the famous Grand Dame of Death, Scythe Curie. Citra fails accidentally, prompting Rowan to fail intentionally out of solidarity. Rand, one of Goddard’s scythes, argues that the bond between Citra and Rowan is too strong and that the winner of Faraday’s contest should glean the loser to ensure it remains a healthy competition. Against Faraday’s strong objections, the High Blade of the MidMerican region, Xenocrates, accepts Rand’s proposal without allowing any debate.  

In the wake of Xenocrates’ shocking decision, Faraday gleans himself. Ordinarily, his act would have freed Rowan and Citra from being his apprentices, thus sparing them from the requirement that one kill the other. However, other scythes come forward to take over their training. Curie claims Citra while Goddard requests Rowan, and both must continue their training. Though Citra is initially horrified by the sudden, random manner by which Curie selects those she gleans, she eventually realizes that Curie is just as principled as Faraday had been, though in her own way. Despite Citra and Curie’s growing closeness, Citra undertakes a secret investigation to determine what really happened to Faraday. Rowan, meanwhile, lives in a luxurious mansion with Goddard and his cruel associates. Goddard subjects Rowan to a brutal beating to initiate him, while also lavishing him with material goods and praise.  

Despite his distaste for Goddard and his own private decision to allow Citra to win the apprenticeship, Rowan finds himself drawn to some aspects of Goddard’s philosophies. As Rowan’s training progresses, he begins killing live subjects, though Goddard arranges for their revival afterward. Eventually, Goddard brings Rowan along on mass gleanings. Rowan secretly tries to help save as many people as he can during the massacres, though he is filled with self-loathing afterward. When Citra and Rowan meet at the year’s second Conclave, Citra shares her theory with Rowan that Goddard murdered Faraday, but Rowan does not believe her. Soon, they face off in a Bokator martial arts match for their final test. Rowan tries to throw the contest in order to save Citra, but she keeps allowing him to win. In a desperate bid to lose, Rowan breaks Citra’s neck, temporarily killing her until she can be revived, and gets himself disqualified through a technicality. Their test is postponed to the next Conclave. 

At a party, Rowan watches Goddard manipulate and humiliate Xenocrates. Afterward, Rowan asks Goddard whether he killed Faraday, and Goddard quickly intuits that Citra suspects him. Just as Citra informs Curie of her suspicions, Xenocrates has Citra arrested and accuses her of killing Faraday. Under pressure to sign a false confession, Citra jumps off a skyscraper, temporarily killing herself. While in a state between life and death known as being “deadish,” Citra communicates with the Thunderhead. Though it cannot intervene, the Thunderhead worries about the direction Scythedom is going and warns Citra she may play a role in the future. When she asks what happened to Faraday, the Thunderhead cryptically reveals a name to her, Gerald Van Der Gans. Citra wakes up far away from her home to find that Curie has taken her into hiding. Curie confesses she and Faraday were once lovers but also warns Citra that she will have to go on the run, and that she will be on her own. Citra tracks down Gerald Van Der Gans and is stunned to realize it is Faraday himself, who faked his gleaning and had no clue the Conclave had not released Citra and Rowan from their apprenticeships.  

In the leadup to the final Conclave of the year, Citra returns home after Curie clears her of the accusations against her. During a mass gleaning where Goddard tries to pressure Rowan into gleaning someone, Rowan instead gleans Goddard and his associates. Rowan destroys their remains with fire to prevent them from being revived and then claims it was an accident. Xenocrates doesn’t believe Rowan but decides to call off an investigation when Rowan returns Xenocrates’ illegitimate daughter, whom Goddard had kept as a hostage, to him. During the next Conclave, Citra realizes the final test to become a scythe involves killing a relative. Though she struggles with the morality of it, she compassionately kills her brother and learns he will be revived later. Citra is announced as the winner of the contest, and she takes the unorthodox name Anastasia. Rather than gleaning Rowan, Citra punches him in the face, causing Rowan’s lips to touch her scythe ring. By rule, kissing a scythe’s ring confers immunity from gleaning, so Rowan is spared. After confessing their love for each other, Citra helps Rowan escape with Faraday and go into hiding. She later learns of a rogue, un-ordained scythe called Lucifer who kills corrupt scythes with fire. She is certain Lucifer is actually Rowan and hopes that he will spare her as she once spared him.