Three children live with their alcoholic and abusive father, three years after a lightning storm sent their mother away. After spending those years being terrible to his children, the father has a change of heart and wants to become a better man.
In Matthew 5:29–30, it says: If your right eye makes you stumble, tear it out and throw it from you; for it is better for you to lose one of the parts of your body than for your whole body to be thrown into hell. If your right hand makes you stumble, cut it off and throw it from you; for it is better for you to lose one of the parts of your body, than for your whole body to be damned.
The father decides to take the verses of Matthew literally.
To do this, he enlists the help of The Collector, a young male doctor who amputates the feet, eyes, tongue, ears, and hands of bad people to be replaced with those of someone better.
The oldest daughter is tasked with the amputations, sawing off her father's limbs in their old shed. She trades each old part with The Collector for a new one to sew on.
Once the process is nearly over, the father reveals the true nature of the situation: the parts his daughter has been sewing onto him belonged to her mother. She wants revenge on the doctor.
When she goes to their house, she discovers an open front door with a room full of dioramas waiting for her. They are made of the gingerbread men she always baked for The Collector, the figures spelling out the full story. The Collector's mom had died jumping from a burning building. The doctor, believing in bird folklore (that wrens deliver spirits—a theme carried throughout the story) tried to turn his son (The Collector) into a bird.
The son's plan all along was to somehow get himself back, carried through when the daughter kills the doctor and gives the son his face and limbs.