After accidentally breaking a statue of a kappa at a shrine in Asakusa, middle school student Kazuki Yasaka encounters Keppi, heir to the throne of the Kappa Kingdom. He, along with his classmates Toi Kuji and Enta Jinnai, enrage Keppi by calling him a frog; he steals their shirikodama, a mythical organ located in the anus that stores an individual's desires, and transforms them into kappas. Keppi informs them they must defeat a zombie by extracting its shirikodama in order to become human again. They are successful, but the act of "Sarazanmai" to transfer the shirikodama to Keppi exposes Kazuki's secret to the group: that he cross-dresses as the idol Sara Azuma. In a post-credits scene, police officers Reo Niiboshi and Mabu Akutsu extract the desires of a man they are questioning.

Keppi gives the group a Dish of Hope as thanks for helping him, which grants one wish to whomever possesses it, and informs them that they can earn more plates by defeating more zombies. Kazuki explains that he cross-dresses for his younger brother Haruka, a fan of Sara's, and that he wishes to earn a dish for him. Toi wishes to earn a dish for his older brother Chikai, a yakuza for whom he sells cannabis. Kazuki and Toi are later forced to pursue Nyantaro, a feral cat cared for by Kazuki and Haruka, after he steals a bag of cannabis from Toi's grow-op. Nyantaro is suddenly captured by a kappa zombie who, upon being defeated, exposes Kazuki's secret that Nyantaro is domestic cat that he stole. In a post-credits scene, Enta encounters a sleeping Kazuki dressed as Sara, and kisses him.

Enta, who has a crush on Kazuki, wishes to earn a dish so that Kazuki will return to playing soccer with him. Reo and Mabu extract the desires of Otone's boyfriend (who, unbeknownst to her, is a serial killer targeting women) and turn him into a zombie. The group defeats the zombie, exposing the secret of Enta's crush, and causing Otone to forget her boyfriend ever existed. In a post-credits scene, Enta visits Haruka in a hospital, who is revealed to be a wheelchair user.

Kazuki asks for Toi's help to kidnap Sara and so that he can take her place during a meet-and-greet that Haruka plans to attend. Toi's backstory is revealed through a flashback – after his parents died from suicide upon being conned into crippling debt, the family's soba shop was saved from closure through Chikai's intervention. When a yakuza came to collect the family's debt, he was shot by Toi, which was subsequently covered up by Chikai.

The group rescue Haruka after he is kidnapped by Reo, and are transformed back into human form. Keppi explains that Reo and Mabu are agents of the Otter Empire, who have been at war with the Kappa Kingdom for generations over the energy of the shirikodama; with the Kappa Kingdom now defeated, the Otter Empire has begun to extract the shirikodama of humans. In a post-credits flashback set during the Otter-Kappa war, Mabu sacrifices himself to protect Reo in battle.

In a flashback, Mabu is brought back to life with a mechanical heart transplanted by Otter, though Reo believes that Mabu is merely a re-animated facsimile. Chikai's criminal dealings force him to flee the city, and Toi announces that he intends to join his brother. The group agrees to use the dishes to help Chikai, but discover they have been stolen. Upon defeating a kappa zombie, Enta is exposed as having stolen the dishes out of jealously over Kazuki's concern for Toi.

Chikai and Toi make preparations to leave the city. Enta returns the Dishes of Hope to Kazuki, but they are confronted by Reo and Mabu, who intend to use the dishes to restore Mabu. Reo shoots Enta, and takes the dishes.

Keppi transforms a hospitalized Enta into a kappa so that he and Kazuki can recover the dishes. Reo witnesses Otter performing sexually-charged "maintenance" on Mabu's heart; when he intervenes, Otter appears in the form of Reo, and explains that he is a mirror of Reo's inner desires. Meanwhile, Chikai is shot and killed in a confrontation with the yakuza.

Kazuki, Enta, and Keppi encounter Dark Keppi, the corporeal form of half of Keppi's shirikodama held by the Otter Empire. Otter, having learned of Reo's plan to use the dishes on Mabu, transforms Mabu into a zombie. Keppi transforms Reo into a kappa, who recovers Mabu's shirikodama and learns that Otter forced Mabu into giving up his connection with Reo in order to live. Mabu tells Reo that he loves him, causing his mechanical heart to explode. A grieving Reo attacks Kazuki, Enta, and Keppi, but is shot and killed by Toi, who wishes to use the dishes to bring Chikai back to life. Kazuki uses the dishes to save Enta's life, and Toi is absorbed by Dark Keppi.

Toi begins to destroy his connection to Kazuki and Enta, but ultimately chooses to preserve it. Keppi fuses with Dark Keppi, with assistance from the group and a revived Reo and Mabu, and defeats Otter and the concepts it represents. Upon performing sarazanmai, Kazuki, Toi, and Enta foresee a potential future in which their connections to each other are eventually severed. In the aftermath, Toi is sent to juvenile detention for three years. Upon his release, he jumps off of the Azuma Bridge, but is rescued by Kazuki and Enta. The three happily run "off to the future" together.