The film opens with a short clip showing the parasitic life cycle of cuckoos, who lay their eggs in the nests of other birds. Once hatched, the cuckoo pushes the mother bird's young out of the nest and is then tended to by the surrogate mother. By the end of the clip, the cuckoo is disturbingly larger than the mother bird, greedily eating all she has to offer.
Young couple Tom and Gemma want to purchase a house. They visit a strange real estate agent, Martin, who tells them of a new development called Yonder. Gemma and Tom drive out to the development with Martin, where the houses there are identical suburban homes. The place is silent, empty, and otherworldly. Martin shows the couple around house #9 and then vanishes. Gemma and Tom attempt to leave Yonder but become lost; every route returns them to #9. The car eventually runs out of fuel and they decide to stay the night in #9.
The next morning, Tom climbs onto the roof to see if he can spot a way out of Yonder. He sees that the houses of Yonder seem to stretch into infinity. The couple decide to follow the artificial-looking sun, hoping it will lead them out if they stay on course. The couple, however, is still led back to #9. They find a delivery box filled with prepacked food and other necessities. A furious Tom sets #9 ablaze, hoping to attract attention. The exhausted couple falls asleep and awakes outside a rebuilt #9 to find a tiny infant in a box with instructions: "Raise the child and be released."
Three months later, the infant has rapidly grown to the size of a seven-year-old boy with an adult-like voice, imitating Tom's and Gemma's. He incessantly demands attention, emitting a high-pitched shriek when his needs are not met, and closely observes and mimics the couple when he is not absorbed by strange patterns on the television. Living with the boy and their strange imprisonment takes a psychological toll on the couple. Their physical well-being also worsens. Tom discovers that the soil of Yonder is made from a seemingly artificial substance. He starts to dig a hole and becomes obsessed. Digging makes him feel as if he has a purpose, but the hole just gets deeper and deeper. When he hears noises at the bottom of the hole, he continues digging.
Tom's health, physically and mentally, deteriorates further. He attempts to kill the boy by locking it in the car until their captors come to rescue it or it starves, but Gemma eventually intervenes. She then attempts to understand their predicament by engaging with the boy. She discovers that he is incapable of imagining things or dreaming. Tom's emotional distance pushes her closer to the boy. One day, the boy vanishes, only to reappear with a strange textbook in an unknown language, with illustrations of humanoid beings with large throat sacs. Gemma asks the boy who gave the book to him, and he shows her by inflating his throat sacs and making alien sounds.
After more time has passed, Gemma and Tom have grown weaker. The boy has grown into an adult and Gemma and Tom reunite in their fear of him. The boy leaves the house every day, and Gemma loses track of him when she tries to follow. While digging, Tom finds a withered corpse in a body bag, and afterward, he dies in Gemma's arms while reminiscing about the first time they met. The boy approaches later with a body bag, sealing Tom's body inside and dumping him into the hole. A vengeful Gemma attempts to kill the boy with Tom's pickaxe the next morning, but she only manages to injure him. Hissing and crawling like an insect, he flees into a bizarre pocket underneath the curb. Gemma follows and tumbles through parallel homes where other young couples are shown living lives of similar despair. Gemma is then spat back out into #9.
The boy explains that a mother's purpose is to raise a child and then die. After a final act of verbal defiance, Gemma gives up. The boy buries her alive in the hole with Tom and leaves Yonder. He then becomes an estate agent, replacing Martin, who has finished his life cycle. The new Martin rolls up his predecessor's body and places it into a filing cabinet before assuming his new position. A new couple walks into the office and Martin rises to greet them.