Gemma, Imogen Poots and her boyfriend Tom, Jesse Eisenberg, a landscaper, confront the unsettling aftermath of a cuckoo’s brood parasitism as they bury the altricial chick that was ejected from its nest.
They later visit a housing development called Yonder, where all the homes look identical, and they are shown house number 9 by an unusual real estate agent named Martin, Jonathan Aris, who unsettlingly mimics Gemma's answer after asking if they have children. After a tour, Martin disappears without explanation. Gemma and Tom try to leave the development, but somehow end up back at house 9, and the couple drives through the seemingly endless, identical streets until they finally run out of fuel.
Back at the house, they sleep inside and attempt to escape on foot, but every exit funnels them back to the same place. Outside, they discover a box containing vacuum-sealed, flavorless food. Tom sets the house on fire, and the couple sleep on the pavement. By morning, the fire has left no damage, and another box appears, this time containing an infant, Côme Thiry, along with a message instructing them to raise the child in order to be released.
After 98 days, the child has grown rapidly to the size of a ten-year-old, mirroring Tom and Gemma and shrieking when hungry. When the child calls Gemma “Mother,” she denies the role, while Tom refers to the child as “it.” The couple waits in the garden with a pickaxe to ambush whoever is delivering the food, but no one appears. Tom begins digging a hole in the garden while growing withdrawn. Meanwhile, the Boy watches abstract, fractal-like patterns on television.
Tom locks the Boy in their car in an attempt to lure whoever is responsible. However, Gemma takes pity and releases the Boy. Tom continues digging and starts sleeping in the hole. One day, the Boy disappears and returns with a strange book filled with symbols and drawings of humanoid figures with throat sacs. When Gemma asks him to mimic the person who gave him the book, the Boy makes rasping sounds and inflates his own throat sacs.
The Boy matures into a young adult, and Tom becomes ill. The Boy leaves each day, and Gemma tries to follow him but always finds herself back at number 9. Tom keeps digging and eventually discovers a corpse in a vacuum bag. The Boy locks Gemma and Tom out of the house, and they sleep in the car. Gemma pleads for medicine for Tom, but the Boy replies, “Maybe it's time he was released.” Tom dies, and the Boy zips him into a vacuum bag and tosses it into the hole.
Realizing that release means death, Gemma wounds the Boy with the pickaxe. The Boy hisses and crawls into a labyrinth beneath the sidewalk. Gemma follows and crashes through a door into multiple rooms in other houses, where she encounters more Boys and several strangers, one of whom has committed suicide.
She lands back at number 9, weak and moaning. The Boy is there, cleaning the house, and carries her to a vacuum bag, explaining that mothers die after raising their sons. She dies as he zips her in. The Boy buries her with Tom, and the grass reforms over the grave. He drives back to the real estate office, where an aged Martin lies dying. Martin gives the Boy his name tag and dies. The Boy zips Martin into a vacuum bag and conceals him in a garbage chute disguised as a file drawer. When a couple walks in, the Boy greets them just as Martin did.
