"Shadows House" is a gothic mystery anime set in a sprawling mansion inhabited by the aristocratic Shadows, enigmatic beings who exude soot instead of breathing. The Shadows are served by living dolls, who act as their caretakers and are tasked with cleaning the soot they produce. The dolls also serve as "faces" for the Shadows, who lack distinct features. The story centers on Emilico, a cheerful and curious living doll, and her master, Kate, a Shadow who is gentle and inquisitive. Emilico and Kate share a close bond, with Emilico striving to understand Kate's needs and emotions despite the inherent mysteries of their relationship.

The narrative unfolds as Emilico and Kate navigate the hierarchical and secretive world of the Shadows House. The mansion operates under strict rules, with the Shadows and their dolls preparing for a ritual called the "Debuts," where they must prove their worth to ascend in status. However, the process is fraught with tension, as failures during the Debuts result in the disappearance of both Shadows and their dolls. As Emilico and Kate interact with other Shadow-doll pairs, they uncover unsettling truths about the mansion's purpose and the origins of the Shadows.

Key characters include Shaun and John, another doll-Shadow pair who become allies to Emilico and Kate. Shaun is diligent and loyal, while John is brash but protective. Other notable pairs include Lou and Louise, who embody elegance and grace, and Ricky and Patrick, whose relationship is strained by Patrick's aloofness. The story delves into the dynamics between the dolls and their masters, exploring themes of identity, loyalty, and autonomy.

As the plot progresses, Emilico and Kate uncover a darker side to the Shadows House, including the existence of a "morph" process that transforms dolls into Shadows and the manipulation of the dolls' memories. The series builds tension through its exploration of the mansion's secrets, the moral ambiguities of the Shadows' existence, and the growing resistance among some dolls to their predetermined roles. The narrative balances moments of lighthearted camaraderie with an underlying sense of dread, creating a compelling mystery that keeps viewers engaged.