The following version of this book was used to create this study guide: Vandermeer, Jeff. Borne. Farrar, Straus and Giroux, 2017.

In an unnamed post-apocalyptic city menaced by a giant flying bear named Mord, the narrator Rachel discovers a strange object that she comes to call Borne. At first glance, Borne appears to be a cross between a vase and a sea anemone, and he is tangled in Mord's fur. Rachel takes Borne to her home, an abandoned hotel called the Balcony Cliffs, where she lives with her friend and lover, Wick. Wick is a drug dealer, selling memory beetles to his clients which, when ingested, allow for the erasure of painful memories. Wick used to work for the Company, a sinister organization that once governed the city and that is responsible for creating Mord, along with other biologically engineered creatures the characters call “biotech” (120). The Company is now just a shell of a building in the city with a few survivors camped out inside. Wick has a professional rival named called the Magician who also used to work for the Company; the Magician has plans to take control of the city herself. Rachel grew up on an island with her parents, and then traveled with them seeking safety as the apocalypse ravaged the world. She cannot remember how they died or how she came to the city.

Shortly after bringing Borne home, Rachel is attacked in the Balcony Cliffs by a group of violent feral children. After they leave, Borne speaks to Rachel for the first time. Borne begins to change in appearance, sprouting eyes and growing ever larger. He tells Rachel that he killed the children who attacked her. Wick warns Rachel that Borne might have come from the Company, and could be dangerous, but Rachel ignores these warnings, as she has begun to love Borne.

Borne asks for his own apartment in the Balcony Cliffs. He and Rachel go out into the city and hide on the rooftop of an abandoned factory when they hear a group of feral children approaching. Rachel watches through a hole in the roof as the children are set upon by Mord proxies, smaller, more vicious versions of the giant flying bear. The proxies annihilate the children, and one heads toward the roof. Borne disguises himself as a giant rock surrounding Rachel, keeping her safely inside himself. When they return to the Balcony Cliffs, Wick again warns Rachel that Borne is a danger to them. He also tells her that the Magician has demanded they give her the Balcony Cliffs and everything in it, and that he has to do as she says, because he is ill and she gives him the medicine he needs to survive. After having seen the Magician's insignia on one of the children in the factory, Rachel realizes that the children who attacked her worked for the Magician, and that Wick knew this all along.

One day, Wick takes Rachel to the roof of the Balcony Cliffs, because he heard the Magician was planning something. They watch as her people fire a missile from her stronghold, striking Mord in the head and injuring him. Later, when Rachel is unable to sleep, she visits Wick during the night, and sees herself there, already talking to him. She realizes that Borne has been disguising himself as both her and Wick. He was doing this to try to make peace between them, but Rachel feels violated and tells Borne he must leave the Balcony Cliffs, though it breaks her heart to do so. Once he is gone, Rachel goes through his room and finds a journal in which Borne admits that he must kill and consume his prey in order to survive, and that he has struggled to control his impulses and to not hurt Rachel.

Shortly thereafter, Rachel and Wick are chased out of the Balcony Cliffs by Mord proxies. They rest briefly in a nearby well, where Wick realizes he has left his medicine behind. They must go to the Company building in search of more medicine. Wick gives Rachel a letter that she is to read in the event of his death. On the way to the Company building, Borne visits Rachel and tells her that he has been killing Mord proxies and evil people only, and that he has a plan to make everything better. He then disguises himself as Mord, and goes chasing after the giant bear. They begin to clash.

Inside the Company building, Rachel finds the medicine and gives it to Wick, whose condition is rapidly deteriorating. She follows a set of footprints into a room with a giant silver portal on one wall. The Magician is there, and explains that the Company used the portal to get supplies into the city. She asks Rachel to join her cause to take over the city. Instead, Rachel kills her, beating her over the head with a rock. Inside the room with the portal, Rachel discovers boxes and boxes of identical Bornes, as well as discarded human-like biotech, all of which have Wick's face. She was prepared for this, as she had already read his letter, in which he admitted that he was not human. He further told her in the letter that he had given her memory beetles at her request to make her forget the deaths of her parents, who were killed by Company employees after having entered the city by stowing away in boxes.

Back outside, Rachel and Wick watch as Borne defeats Mord by transforming into a sea-like expanse of skin and absorbing Mord. They both disappear. In the aftermath, the city sprouts new plant and animal life. Rachel and Wick return to the Balcony Cliffs, but they invite others to join them. Having learned to love and nurture from her experience with Borne, Rachel becomes a mother figure to some orphaned children.