"Breakfast with My Two-Tailed Cat" centers on the life of a young man named Haruto, who lives a quiet, uneventful existence until he encounters a mysterious two-tailed cat named Neko. Neko is no ordinary feline; she possesses the ability to transform into a human girl, revealing herself as a supernatural being with ties to ancient folklore. Haruto reluctantly takes her in, and their lives become intertwined as they navigate the challenges of cohabitation and the peculiarities of Neko's dual nature.

The narrative explores the dynamics of their relationship, blending slice-of-life moments with supernatural elements. Neko's presence disrupts Haruto's routine, introducing him to a world of magical occurrences and mythical creatures. As their bond deepens, Haruto learns more about Neko's origins and the responsibilities tied to her existence as a guardian spirit. The story delves into themes of companionship, trust, and the blending of the mundane with the extraordinary.

Supporting characters include Haruto's friends and acquaintances, who gradually become aware of Neko's true identity, as well as other supernatural entities that either aid or challenge the duo. The plot balances lighthearted, comedic interactions with moments of tension and emotional depth, particularly as Haruto and Neko confront external threats and internal conflicts. The series maintains a steady pace, alternating between episodic adventures and overarching storylines that reveal more about the world Neko inhabits and the role Haruto plays within it.