"My Deer Friend Nokotan" centers around Torako Koshi, a high school girl whose life takes an unexpected turn when she encounters Nokotan, a mysterious deer-human hybrid. Nokotan, who appears to be a cheerful and eccentric character, quickly becomes a central figure in Torako's daily life. The series explores their growing friendship and the peculiar situations that arise from Nokotan's presence.

The narrative unfolds in a school setting, where Torako navigates the challenges of adolescence while dealing with Nokotan's antics. Nokotan's unique abilities and deer-like traits often lead to humorous and surreal scenarios, blending slice-of-life elements with fantastical undertones. The dynamic between Torako and Nokotan is a key focus, highlighting themes of acceptance, friendship, and the blending of the ordinary with the extraordinary.

Supporting characters include Torako's classmates and teachers, who react in various ways to Nokotan's presence. Some are bewildered, while others embrace the oddity, adding layers of interaction and conflict. The series balances comedic moments with quieter, introspective scenes, creating a multifaceted portrayal of its characters' lives.

The plot progresses through episodic adventures, each highlighting different aspects of Torako and Nokotan's relationship. These episodes often incorporate elements of Japanese folklore and mythology, subtly enriching the story's cultural backdrop. The interplay between the mundane and the fantastical is a recurring motif, emphasizing the series' unique tone and narrative style.

Overall, "My Deer Friend Nokotan" presents a whimsical yet grounded tale of friendship and self-discovery, set against a backdrop of everyday life infused with magical realism. The characters' development and their interactions drive the story, offering a blend of humor, heart, and a touch of the surreal.