Junpei Kousaka, a high school student with a strong aversion to cats due to a childhood allergy, finds his life turned upside down after accidentally breaking a statue of the cat deity Nyanmaru. As punishment, he is cursed with the ability to understand and speak to cats. The curse comes with a dire condition: if Junpei fails to grant the wishes of 100 cats within a set timeframe, he will be transformed into a cat himself. This predicament forces Junpei to confront his fear and dislike of felines while navigating the chaos that ensues from his newfound ability.

Junpei’s life becomes increasingly complicated as he interacts with various cats and their often absurd or heartfelt wishes. Along the way, he encounters a colorful cast of characters, including Kaede Mizuno, his childhood friend and secret crush, who is unaware of his curse. Kaede’s love for cats contrasts sharply with Junpei’s predicament, creating both comedic and heartfelt moments. Another key figure is Kanako Sumiyoshi, a wealthy and eccentric classmate who harbors feelings for Junpei and often competes with Kaede for his attention. Her over-the-top personality and schemes add to the series’ comedic tone.

The narrative balances humor, romance, and supernatural elements as Junpei struggles to fulfill the cats’ wishes while managing his relationships and personal life. The cats themselves play a significant role, each with distinct personalities and desires that drive the plot forward. From helping a stray cat find a home to resolving conflicts between feline rivals, Junpei’s journey is filled with challenges that test his patience, empathy, and resolve.

As the story progresses, Junpei’s interactions with cats and humans alike lead to personal growth, gradually shifting his perspective on felines and deepening his connections with those around him. The series explores themes of responsibility, compassion, and the unexpected ways in which lives can intertwine, all while maintaining a lighthearted and comedic tone. The curse serves as both a narrative device and a metaphor for overcoming personal fears and prejudices, making "Nyan Koi!" a blend of supernatural comedy and character-driven storytelling.