"Magical Nyan Nyan Taruto" centers on Taruto, a young cat-girl living in a world where anthropomorphic cats coexist with humans. Taruto is an orphan raised by a kind human named Iori, who runs a bakery. Despite her cheerful demeanor, Taruto harbors a mysterious power tied to her origins, which she is unaware of at the story's outset. Her life takes a dramatic turn when she encounters Chitose, a magical cat from the Cat Kingdom, who reveals that Taruto is the reincarnation of the Cat Princess, a figure of great importance to their realm.

The Cat Kingdom is under threat from an evil force led by the malevolent cat Karuto, who seeks to exploit Taruto's latent powers for his own gain. Chitose tasks Taruto with mastering her magical abilities to protect both the Cat Kingdom and the human world. Alongside her friends, including the loyal and protective cat Kansuke and the mischievous but kind-hearted kitten Kiri, Taruto embarks on a journey of self-discovery and growth. As she learns to control her powers, she faces numerous challenges, including battles with Karuto's minions and internal struggles about her identity and purpose.

The narrative blends elements of fantasy, adventure, and comedy, with a focus on themes of friendship, courage, and self-acceptance. Taruto's journey is marked by her evolving relationships with her companions and her gradual understanding of her role as the Cat Princess. The story balances lighthearted moments with more serious undertones, particularly as Taruto confronts the darker aspects of her destiny and the responsibilities that come with her powers. The series concludes with Taruto embracing her true self and fulfilling her role as a protector of both worlds, solidifying her place as a beloved and heroic figure.