This novel is set in Kyoto, Japan, and comprises four interconnected stories. Each centers on a person who finds their way to Nakagyō Kokoro Clinic for the Soul, a mysterious psychiatric clinic staffed by a whimsical doctor named Nikké and a stern nurse named Chitose. Rather than conventional therapy, the doctor prescribes cats, and each patient's relationship with their prescribed cat becomes a catalyst for emotional change. The final chapter reveals the true nature of the clinic and its staff.
In the first story, Moé Ohtani, a college student, wanders into a dark alley while brooding over signs that her boyfriend, Ryuji, is about to break up with her. She discovers the clinic after Dr. Nikké calls down to her from a window and playfully threatens to jump, prompting her to rush inside. When she admits she does not want to be separated from the person she loves, the doctor prescribes her a cat: Kotetsu, a four-month-old Bengal. He instructs her to take the cat home for one week and record its diet and excretions in a journal called the Cat Record.
Moé struggles with Kotetsu's care, and when Ryuji visits, the cat kicks litter and feces into his face, causing him to leave before delivering whatever talk he had planned. Her closest college friend, Reona Kajiwara, who owns a cat named Hajime, helps Moé with feline care. After returning Kotetsu, Moé is prescribed a second Bengal, Noelle, whose litter-box distress Reona diagnoses as a problem of proximity between food and litter tray. When Moé tries to find the clinic again, she cannot locate the building, and no online search yields results.
A third cat follows: Bibi, a six-year-old retired show cat who refuses commercial food and will not let Moé approach. Reona suggests he needs exercise, and after an intense play session with teaser wands, Bibi devours his food eagerly. When Ryuji arrives unexpectedly, Moé confronts him about wanting to end their relationship. Ryuji is baffled: He reveals he is being transferred to Tokyo and has been distant only because he worried she could not handle being alone. Moé realizes she escalated a misunderstanding by avoiding direct communication. The doctor's principle that what goes in must come out, a lesson about feline digestion, becomes a metaphor for emotional honesty.
The second story follows Tatsuya Satonaka, a 78-year-old widower who has grown lethargic since his wife, Meiko, died of a stroke six months earlier. He also worries about his 17-year-old grandson, Hayato, who has become nocturnal and barely leaves his room. Urged by his daughter-in-law to seek help, Tatsuya heads to the clinic building but cannot manage the stairs and is carried up by Akira Shiina, a boisterous man who runs a magnetic necklace business on the fifth floor. Shiina insists the neighboring unit is vacant, formerly the site of an illegal cat-breeding operation where animals were abandoned.
Inside, Dr. Nikké remarks that cats navigate darkness by focusing only on what they need to see. He drapes an enormous black-and-white cat, part Maine Coon, over Tatsuya's shoulders. Tatsuya notices the cat's tight pink collar and asks the doctor to remove it. When Tatsuya leaves, Chitose insists he take the collar with him.
That night, leg cramps send Tatsuya on his first walk since Meiko died. He spots a bulletin board flyer for a missing cat named Ms. Michiko, whose description matches the clinic cat exactly. Hayato appears on his bike, returning from night school, a fact Tatsuya did not know. Using social media, Hayato traces the cat to a foster family in Shiga Prefecture. Grandfather and grandson travel there by train, confirm the identification with the pink collar, and return Ms. Michiko to her owners. Tatsuya takes on roles in the neighborhood association, and Hayato begins digitizing their records.
The third story shifts to Reona, Moé's friend, who resents her mother's favoritism toward Reona's older brother, Tomoya, a 29-year-old deputy director of a cat rescue center. Reona's childhood friend, Shousuke Kunieda, reveals he has visited a clinic where the doctor looked exactly like Tomoya and was prescribed a short-legged Munchkin kitten named Shasha. Shousuke has decided to abandon his years-long attempt to pass the Kyoto University entrance exam, and Reona accompanies him to return the kitten.
At the clinic, when Dr. Nikké asks what brings her in, Reona blurts out, "I think I hate my mom" (165). Despite her protests, the doctor prescribes Shasha to Reona for 10 days alongside Hajime. To secure her mother's approval, Reona claims the kitten came from Tomoya's rescue center. The two cats' comic confrontation and eventual affection bring Reona and her mother together in laughter. Her mother reveals that Tomoya once brought home a black kitten, but young Reona was frightened by it because of a villainous cat in a manga, so Tomoya returned it and got Hajime instead. Reona realizes her forgotten childhood fear altered her brother's bond with cats. After developing pyelonephritis, a kidney infection caused by dehydration during a work shift, Reona is hospitalized overnight with her mother at her bedside. She decides to adopt Shasha permanently.
The fourth story centers on Tomoya himself, who dreads returning home each evening because his black rescue cat, also named Nikké, lies perpetually asleep in a stainless steel pen. Three years earlier, Tomoya rescued the cat from the very building that now houses the clinic, where an illegal breeder had abandoned dozens of cats. Only Nikké and a female calico survived. About a year ago, the cat stopped waking even when lifted, though he continues to eat and drink during the day when Tomoya is away.
After rushing a pregnant stray to Dr. Kokoro Suda's veterinary practice for an emergency cesarean, Tomoya wanders into the clinic. When Dr. Nikké tries to prescribe a cat, Chitose announces they have none available and declares that Tomoya already has his prescribed cat at home. For five days, the cat awakens each evening, and Tomoya is overjoyed. Then Nikké falls motionless again. Panicking, Tomoya rushes the cat to Dr. Suda and confesses the truth: He has been terrified every day of finding Nikké dead and has deliberately avoided being home. His deepest wish, the one he is ashamed to voice, is that Nikké will die while Tomoya is present so the cat will not be alone.
Tomoya returns to the clinic, where Dr. Nikké tells him the cat will not wake again. He assures Tomoya that cats possess the strength to pass away while dreaming of happy things, even if completely alone. Chitose bursts through the curtains, demanding the doctor fight for his life. Before Tomoya leaves, Chitose quietly reveals that she, too, died alone, but "it wasn't cold, and it wasn't lonely. I stayed with my special person until the very end" (281-282). This, she says, is what it means for a cat to love a person.
In the closing sequence, the narrative shifts to Dr. Nikké's perspective, confirming that the doctor and Chitose are themselves the cats who once lived in this room when it was part of the breeding facility. He remembers gentle hands that eventually stopped coming. Chitose corrects his earlier characterization of her as a younger sister, insisting that sibling roles reverse after a certain age. She demands he hold on until his remaining patient, a woman named Ao Torii who has abandoned her treatment, is healed. The door opens, a new patient enters, and Dr. Nikké smiles: "We'll prescribe you a cat" (293).