"Misaki-kun wa Kōryaku Chara janai" centers on Misaki, a high school student who is often mistaken for a "capture target" character in a dating sim due to his striking appearance and aloof demeanor. Despite his looks, Misaki has no interest in romantic pursuits and is more focused on his studies and personal goals. However, his life becomes increasingly complicated as his classmates, particularly the female students, begin to project their romantic fantasies onto him, treating him as if he were a character designed to be "conquered" in a game.

The narrative explores the dynamics between Misaki and his peers, highlighting the misunderstandings and assumptions that arise from their perceptions of him. Misaki’s attempts to maintain his individuality and resist being typecast as a romantic interest form the core of the story. His interactions with other characters, including his childhood friend who understands his true personality, reveal the gap between how he is perceived and who he truly is. The series delves into themes of identity, societal expectations, and the pressure to conform to predefined roles, all while maintaining a lighthearted and comedic tone.

The supporting cast includes a variety of archetypal characters, such as the energetic classmate, the shy admirer, and the rival, each of whom contributes to the misunderstandings and comedic situations that Misaki navigates. The story balances humor with moments of introspection, as Misaki reflects on the challenges of being seen as a "character" rather than a person. Through these interactions, the series examines the complexities of human relationships and the impact of preconceived notions on personal connections.