"I'd Rather Have a Cat than a Harem!" centers on Aoi Tohno, a high school student who has grown disillusioned with romantic relationships after witnessing the chaotic and often shallow dynamics of her peers. Preferring the simplicity and companionship of animals, Aoi adopts a stray cat named Mochi, which becomes her primary source of comfort and joy. Her life takes an unexpected turn when she attracts the attention of several male classmates, each with distinct personalities and motivations, leading to the formation of an unintentional harem.

The narrative explores Aoi's struggle to navigate her newfound popularity while maintaining her preference for solitude and her bond with Mochi. Among the suitors is Haruto, a popular and confident classmate who initially approaches her out of curiosity but gradually develops genuine feelings. Riku, a childhood friend, re-enters her life, bringing with him unresolved emotions and a deep understanding of her past. Meanwhile, Kaito, a quiet and introverted student, finds solace in Aoi's company, drawn to her straightforward nature.

As the story progresses, Aoi's interactions with these characters highlight her internal conflict between her desire for independence and the growing connections she forms with others. The series balances lighthearted moments, such as Aoi's humorous attempts to avoid romantic entanglements, with more introspective scenes that delve into her fears of vulnerability and loss. Mochi, the cat, serves as a symbolic anchor, representing Aoi's longing for simplicity and unconditional love.

The manga also examines the perspectives of the male characters, providing insight into their individual struggles and motivations. Haruto grapples with the pressure of maintaining his image, Riku confronts his lingering feelings for Aoi, and Kaito learns to open up to others. These dynamics create a multifaceted exploration of relationships, friendship, and personal growth.

Throughout the series, Aoi's journey is marked by her gradual realization that human connections, while complex, can be as rewarding as the companionship she finds with Mochi. The story avoids overly dramatic tropes, instead focusing on realistic interactions and character development. By the end, Aoi's relationships with both her suitors and her cat reflect a nuanced understanding of love, independence, and the importance of balance in life.