"Nekomachi" is set in a quaint, fictional town where humans and anthropomorphic cats coexist in harmony. The narrative centers around Haru, a young human who moves to Nekomachi after inheriting a small, rundown café from his late grandmother. Upon arrival, Haru discovers that the café is a beloved gathering spot for the town's feline residents, who possess the ability to speak and interact with humans on equal terms. The café, named "Whisker Haven," becomes the focal point of the story as Haru strives to restore it to its former glory while navigating the unique dynamics of the town.

The plot unfolds through Haru's interactions with the town's inhabitants, particularly a group of anthropomorphic cats who frequent the café. Among them is Mochi, a mischievous yet loyal tabby cat who becomes Haru's closest companion and guide to the town's customs. Mochi's playful antics often lead to humorous situations, but he also provides emotional support as Haru adjusts to his new life. Another key character is Sora, a reserved and enigmatic black cat with a mysterious past. Sora's aloof demeanor gradually softens as he forms a bond with Haru, revealing hidden depths and a protective nature.

As Haru works to revitalize Whisker Haven, he uncovers the café's significance to the town's history. The café was once a sanctuary where humans and cats forged deep connections, and its decline has left a void in the community. Through a series of episodic adventures, Haru and his feline friends embark on quests to recover lost recipes, repair the café's infrastructure, and rekindle the town's spirit. These endeavors often involve encounters with eccentric townsfolk, both human and feline, who contribute to the café's revival in unexpected ways.

Themes of friendship, resilience, and cultural harmony are woven throughout the narrative. Haru's journey is not just about restoring a physical space but also about bridging the gap between two distinct yet interconnected communities. The series balances lighthearted moments with poignant reflections on loss, identity, and the importance of preserving traditions. By the end of the story, Haru's efforts culminate in the reopening of Whisker Haven, symbolizing the restoration of unity and hope in Nekomachi. The café once again becomes a vibrant hub where humans and cats gather, celebrating their shared history and the bonds that unite them.