In the year 2042, the technological cloud evolved into an entity called “the Thunderhead,” a sentient conglomeration of all the information ever put into computers. Over the years and with the help of the Thunderhead’s abilities, humankind eliminated disease, war, famine and even death. Nanites can heal any damage to human bodies, even aging.
The only way a person can die now is by being gleaned. A selected group of men and women, known as scythes, are allowed kill individuals in order to keep the planet from overpopulation. The Thunderhead does not interfere with their work, nor are they allowed to access its data in order to manipulate who gets gleaned.
Each scythe takes the name of a historical figure. They are supposed to live outside of normal human interaction in order to remain anonymous and relatively free of biases that could influence the people they choose to kill.
Citra, a teenager, is shocked when Scythe Faraday arrives unannounced to her family’s apartment and invites himself to dinner. She and her family are terrified at the thought that one of them might be gleaned. Only Citra has the courage to demand Faraday does it or leave once dinner has been eaten. Faraday admits he is not there to glean any of them, but their neighbor. He allows Citra’s mother to kiss his ring as payment for the dinner he consumed, giving her immunity from gleaning for one year.
Rowan, another teenager, follows Faraday through the halls of his school when the scythe appears there one morning. Faraday explains that he is there to glean Kohl, the star quarterback. Kohl is terrified, and although he barely knows Rowan, he asks him to stay by his side as Faraday administers the electric shock that kills him. Faraday warns Rowan that although his actions were merciful and showed courage, others will not view it that way. Sure enough, Rowan becomes a pariah as other students spread rumors that he asked the scythe to kill Kohl, or killed Kohl himself.
Several months later, Scythe Faraday requests both Citra and Rowan be his apprentices for the next year. In the end, only one will receive a scythe ring, the sign of their authority and the way in which they grant immunity. The other will be allowed to return to his or her life. Although neither wants to be a scythe, they eventually enter into the apprenticeship with Faraday.
The training is difficult, both mentally and physically. They must learn how to use various weapons, poisons — and even their hands — to kill people. They are taught the history and moral code of the Scythedom. Faraday also instructs them on his own rules of decency, which includes attending the funerals of those he gleans, to show his respect to their family.
Three times a year, scythes gather together for a Conclave, in which they test apprentices and discipline scythes that have broken the rules. At the Vernal Conclave, Rowan and Citra see the political rift that is opening between old-school scythes like Faraday and his friend Curie, and those of the modern world, like Scythe Goddard. Goddard and his followers do not glean individually. Although nothing has been officially documented, they prefer to glean groups, and their killings are terrifying and often painful. Goddard is charismatic, however, and easily deflects all accusations.
In their first tests as apprentices, Scythe Curie questions both Citra and Rowan. When it’s obvious they have formed a friendship, one of Goddard’s followers asks that Faraday not be allowed to have two apprentices, as they appear to be helping each other. She suggests that in order to make sure Citra and Rowan both try their best to become scythes, whoever wins should have to glean the other as their first act as a scythe.
Faraday vehemently objects but is overruled by the scythe’s High Blade, Xenocrates. Scythe Faraday, in an effort to save his apprentices from this decision, commits suicide by jumping in front of a subway train. Usually, when a scythe dies, their apprentice is set free. However, High Blade Xenocrates gives his permission for Citra to be Scythe Curie’s apprentice, while Rowan will apprentice under Scythe Goddard. Looming over Citra’s and Rowan’s training is the reality that the one chosen to be scythe will have to kill the other.
Like Faraday, Scythe Curie believes in the old rules of the Scythedom, and trains Citra in the same manner. Citra doubts that Faraday committed suicide and wonders if the Thunderhead has video evidence of the scene. She investigates in secret, as she knows Scythe Curie would not approve.
Rowan learns a completely different view of Scythedom from Goddard, one of violence, power and entitlement. In order to survive, Rowan develops physically and mentally into a fine-tuned killer, but he knows Goddard’s vision of the scythe is wrong. Of the three scythes that live and work with Goddard, only one, a young man named Volta, seems to have the same misgivings as Rowan.
At the Autumn Conclave, Citra tells Rowan about her investigation into Faraday’s death. She believes he was pushed, and the witnesses who claimed he jumped were offered immunity by the scythe who committed the murder. They both know the scythe who had the most to gain from his death was Goddard, but as they can’t prove anything, they must keep their suspicions to themselves.
As a test of their skills, they are forced to use martial arts to battle each other. Citra knows that Rowan is trying to throw the fight, but refuses to let him. In desperation, Rowan breaks her neck. He does it so that she will not hesitate the next time and win the Scythedom. As the winner, she will have to kill him.
Thinking Rowan has embraced his love of violence, Goddard throws an elaborate party in his honor. Rowan is surprised to see High Blade Xenocrates in attendance. Rowan suspects Goddard is blackmailing the High Blade in order to keep Goddard from being censured by the Scythedom.
Rowan’s friend Volta reveals that Esme, a young girl living in their mansion, is Xenocrates’ illegitimate daughter. Not only would he lose his position should the truth come out, but Goddard has threatened to glean her if the High Blade does not support him.
Once Citra is returned to life, she is arrested for the murder of Faraday. As evidence, a page from Faraday’s journal is brought to light in which he admits to being afraid of a female apprentice. Xenocrates tries to force her to sign a confession, but Citra commits suicide. While she is dead, she is considered a private citizen and not a scythe’s apprentice, thereby putting her under the jurisdiction of the Thunderhead, not the Scythedom.
While she is unconscious and being healed by the nanites, the Thunderhead speaks to her, warning that she will play an important role in the future of the scythes. It also tells her the name of the person who killed Faraday: Gerald Van Der Gans. Scythe Curie manages to help Citra escape from the healing center before she can be arrested again.
Curie explains that in the past, she [Curie] had been Faraday’s apprentice. The journal entry was about her, because he feared her behavior until she admitted she was in love with him. The two broke Scythe law and had an intimate relationship. They were censured, forced to die seven deaths, and then to live without contact for 70 years. As scythe authorities near their hideout, Curie gives Citra a piece of paper with a name and address, and she tells her to flee.
As Citra escapes, she sees the name on the paper is Van Der Gans and believes Curie is sending her to kill Faraday’s murderer. She is shocked when she finds the man and discovers he is Faraday. He faked his death to free her and Rowan, and did not know they were made to continue their scythe apprenticeships. Scythe Curie returns to her home and admits Faraday’s journal page was about her and thereby clears Citra for his murder.
Goddard is furious by this turn of events and leads a deadly rampage against an odd, but harmless, religious cult. Goddard orders his followers to kill every single member, including the children. After his friend Volta gleans himself in despair over his actions, Rowan searches for Goddard. Goddard orders Rowan to kill the last remaining victim. Instead, Rowan runs Goddard through with a sword and takes his scythe ring, effectively making him mortal again. Rowan then cuts off the scythe’s head. He also kills Goddard’s remaining followers and sets the grounds on fire, insuring that even the nanites cannot reanimate the corpses.
Then Rowan denies any part in the scythes’ deaths to High Blade Xenocrates. He brings Esme into the room and intimates he knows her relationship to the High Blade. Xenocrates offers to drop the investigation into Goddard’s death, and Rowan asks him to take Esme home to her mother.
No longer a fugitive, Citra returns to attend the Winter Conclave, but Faraday remains in hiding. On the second day of the Conclave, Citra and Rowan take the stage and wait to see which one will be chosen to be a scythe. Rowan knows if he is chosen, he will kill any scythe that tries to force him to glean Citra.
Citra has her own plan, which she enacts when she is chosen to be a scythe. She puts on her scythe’s ring and then punches Rowan in the mouth for “killing” her in their previous fight. When she then draws her weapon to glean him, her ring, along with all the scythes’ rings, lights up, showing he has immunity.
Just as when a person kisses a scythe’s ring, her ring registered the DNA from Rowan’s bloody lip and gave it to him. Citra points to the tray of knives still on the stage with them and tells him there is a car waiting at the east exit. As the furious scythes try to capture and imprison him, Rowan uses the knives to escape. He gets into the waiting car and is shocked to find Scythe Faraday driving it.
The novel ends with a page from Citra’s journal as the newly renamed Scythe Anastasia. She tells of a rumor that there is someone seeking out corrupt scythes and killing them with fire. Although not an ordained scythe, the public is calling him Scythe Lucifer. She intimates that this Lucifer is Rowan, and hopes he would see her as a good scythe.