In a present-day English town, thirteen-year-old Conor O’Malley is having a recurring nightmare. When he wakes from this terrible dream, he is visited by a monster, which takes the shape of the yew tree next to the church behind Conor’s house. Conor, to the monster’s surprise, is not afraid of the monster. The monster says it is going to tell Conor three stories, after which Conor must tell a fourth story: what happens in his recurring nightmare. Conor is terrified by this prospect.
That morning, Conor completes his daily routine. His mother is sick with cancer, and so he is often left to his own devices to make breakfast, brush his teeth, get dressed, pack his bag, and get himself to school. His mother is upset that he has to do these things for himself because she is so tired, and so she has invited his grandmother to visit and help take care of him, and to take care of her. Conor protests because he doesn’t like his grandmother and thinks that they’ll be fine without her, but his mother insists.
At school, Conor is bullied by a classmate named Harry, alongside his cronies Anton and Sully. Conor’s friend Lily tries to defend him and pushes Sully into a bush, but this only embarrasses Conor further. When a teacher named Miss Kwan asks what’s happening, Conor lies and says that he tripped and Harry was helping him up. Lily gets in trouble for pushing Sully. Walking home that evening, Lily confronts Conor about lying, but he brushes her off. He is angry with her because their mothers are close friends, and when Lily’s mother told her about Conor’s mother’s illness, Lily promptly told other people. After that, all of Conor’s friends and teachers began to treat him differently—mostly by leaving him alone.
Conor’s grandmother arrives. She is very strict with Conor and starts to talk about taking him out of his current school and putting him into a school near her house, which worries Conor because it implies she is talking about a time after his mother has died. Conor’s grandmother also becomes angry with him because he argues that she doesn’t need to be there, but Conor’s grandmother points out that Conor shouldn’t bear the responsibility of taking care of his mother, their house, and himself alone.
That night, the monster tells the first tale. There once was a king, whose sons, wife, and daughter passed away over the course of his life, leaving only his grandson, a young prince, as an heir. The king then remarried a young queen, whom many people suspected was a witch. When the king passed away, the queen wanted to marry the prince in order to retain her throne. But the prince instead ran away with his lover, a farmer’s daughter. One morning on their journey, the prince woke up and saw that someone had murdered the girl and made it look like he did it. The young prince assumed that it was the queen, and rallied the villagers to burn her at the stake. The monster, however, saved the queen from this fate, because it was actually the prince that did it. Conor asks if the lesson he is meant to learn is to be nicer to his grandmother, an idea that the monster laughs off. The monster then explains that the queen was an evil witch, but was not a murderer, and that’s why he saved her. Conor wonders who the “good guy” is in the story—the monster explains that life does not always have a good guy and bad guy.
The next day, Conor’s grandmother tells Conor that his mother has to go to the hospital because her treatments aren’t working. She also tells Conor that his father is coming to visit. (His father and mother are divorced, and he now lives in America with his new wife, Stephanie, and a new baby.) Conor talks to his mother, who assures him that she’s going to be okay—the doctors just need to adjust her treatment.
Conor goes to live with his grandmother for the time being, all the while continuing to have his terrifying recurring nightmare. Conor isn’t exactly comfortable at his grandmother’s house, as his grandmother instates a lot of rules that he’s never had to follow before. When Conor’s father arrives, they go out to dinner, where Conor insists that he’s fine and that his mother is going to be fine. Conor also tells his father that he’s unhappy living with his grandmother, and wonders if he could come live with his father in America. His father says that it wouldn’t be fair to Conor to pull him out of his life in England, but Conor accuses him of simply not wanting Conor to come to America with him.
Conor’s father drops him back at his grandmother’s house, where the monster arrives to tell the boy a second tale. One hundred and fifty years ago, there lived an Apothecary and a parson. The Apothecary dealt in the “old ways of medicine” and was greedy, often overcharging patients for his remedies. The Apothecary asked the parson to cut down the yew tree in the parsonage, because yew trees have healing properties if harvested correctly. The parson refused, and started to preach against the Apothecary because of his use of the “old ways.” But one day, the parson’s daughters fell ill with an infection, and the parson begged the Apothecary to help. He told the Apothecary that he would let him harvest the yew tree, and that he would preach sermons in the Apothecary’s favor. The Apothecary told him that he could not help, and the parson’s daughters died. The monster then destroyed the parson’s house, because the parson was not truly a man of belief and should have given the Apothecary the yew tree when he first asked.
The monster shows Conor the destruction of the parson’s house, and asks if Conor wants to join in. Conor aids in the destruction, but when the monster leaves, Conor can see that he has actually destroyed every inch of his grandmother’s sitting room, which was full of priceless antiques. His grandmother arrives home and screams in horror. But instead of punishing Conor, she pulls down the only display cabinet left standing and goes up to her room, sobbing.
The next morning, Conor’s father visits again to make him breakfast. Conor wonders if he’ll be punished for what he did, but his dad says no, asking, “what could possibly be the point?” His father then tells Conor that his mother has “taken a turn.” When Conor visits his mother in the hospital, she tells him that some of the new treatments haven’t been working. They’re going to try a final option, which is made from yew trees. Conor thinks that this must be why the monster has come: to cure his mother. Conor’s father then tells Conor that he has to fly back to America that night, but before he goes, he tries to be realistic with Conor. He tells Conor that it’s unlikely that the new medicine will cure his mother. Conor accuses his father of abandoning him and his mother, still adamant that his mother is going to be fine.
At school, Conor goes several days without speaking to anyone. He has stopped doing his schoolwork, but the teachers never call on him or ask for his assignments. Meanwhile, he is still angry with Lily. The only connection he has with other students is when Harry, Anton, and Sully come over to bully him. But Harry starts to realize that this is what Conor wants, and so one day at lunch, he simply says to Conor, “I no longer see you.” Conor is outraged, feeling completely helpless and invisible. Then the monster arrives at school to tell the third tale. The third tale is about a man who was invisible because people had become used to not seeing him. And so the monster made the other people see the man. As the monster narrates this story, it beats Harry up, breaking his arm, nose, and several teeth. When it is finished, it tells Conor that “there are harder things than being invisible.”
Conor lands in the headmistress’s office, who is shocked at the damage that Conor did to Harry. Conor tries to argue that the monster did it, but Miss Kwan says that many people saw Conor beating Harry up. The headmistress says that normally Conor would be expelled, but that she could not in good conscience expel Conor given his mother’s illness. Conor returns to class, where students are now terrified of him. He realizes that the monster was right: he is no longer invisible, but he is “further away than ever.”
About a week later, Lily passes a note to him, saying that she misses being his friend, and that she sees him. But before Conor can respond to Lily, he is pulled out of class to go to the hospital. Once there, his mother tells him that her new treatment isn’t working. Conor accuses her of lying, and refuses to look at her or touch her. She tells him that it is okay to be angry. Conor demands to be taken home, and when he arrives he goes to the yew tree behind his house and kicks it, asking the monster why it didn’t cure his mother. The monster says that it did not come to heal his mother, it came to heal him.
The monster says it is time for Conor himself to tell the fourth tale—what happens in his recurring nightmare. Conor enacts the story: his mother is standing on the edge of a cliff when an enormous creature grabs her and tries to pull her down over the edge. Conor holds onto her, feeling her getting heavier and heavier, until he has to let go. The monster tells Conor that he could have held on for longer, but he chose to let her go. Conor admits, through tears, that he always knew she was going to die. He just wants the waiting, pain, and isolation to be over. The monster commends him for telling the truth. Then Conor says that it is his fault that she’s going to die, which the monster says is not true at all. The monster assures him that he only wanted to end his own pain, and that is very human. Conor can want his mother to go and at the same time want to save her, because “humans are complicated beasts.” Conor, comforted, falls asleep in the monster’s nest.
When Conor wakes, his grandmother has been frantically looking for him, and takes him to the hospital because his mother is in very critical condition. At the hospital, Conor tells his mother a final truth: that he doesn’t want her to go. The monster promises to stay with him until the end, and Conor cries, knowing that the end is very near. Conor holds his mother tightly, “and by doing so, he could finally let her go.”