"Kamisama Dolls" is a supernatural action anime set in a world where ancient, god-like mechanical beings known as "Kakashi" are controlled by individuals called "Seishi." These Kakashi are remnants of a secretive, isolated village called the Kuga Village, where they were once used for rituals and protection. The story centers on Kyohei Kuga, a young man who has left his troubled past in the village behind to live a normal life in Tokyo. However, his peaceful existence is disrupted when his estranged childhood friend, Aki Kuga, arrives in the city, bringing chaos and violence with her. Aki, a Seishi with a powerful and destructive Kakashi named Utao, harbors a deep resentment toward Kyohei and seeks revenge for perceived betrayals.

Kyohei is also a Seishi, bonded to a Kakashi named Kukuri, though he initially struggles to control its power. As the conflict escalates, Kyohei is forced to confront his past and the dark secrets of the Kuga Village, including the existence of a rogue Kakashi known as Mahiru, which was created through forbidden rituals and poses a significant threat. Alongside Kyohei is his younger sister, Hibino, who is unaware of the full extent of the village's mysteries but becomes increasingly involved in the unfolding events. Another key character is Utao, Aki's younger sister, who pilots her own Kakashi and serves as a moral counterbalance to Aki's vengeful nature. Utao's innocence and desire for reconciliation contrast sharply with the darker motivations driving other characters.

The narrative explores themes of power, responsibility, and the consequences of wielding forces beyond human understanding. As Kyohei and his allies navigate the escalating conflict, they uncover the truth about the Kuga Village's history, the origins of the Kakashi, and the dangerous ambitions of those who seek to exploit their power. The series balances intense action sequences with moments of introspection, delving into the psychological and emotional struggles of its characters as they grapple with their roles in a world where ancient and modern forces collide.