"Boku wa Shitataka-kun" centers on the life of Shitataka, a high school student whose existence is marked by a peculiar and unsettling condition: he is invisible to everyone around him. This invisibility is not physical but rather a social phenomenon, as people seem to unconsciously ignore his presence. Shitataka navigates his daily life in a state of near-total isolation, unable to interact meaningfully with others or form connections. Despite his condition, he maintains a calm and observant demeanor, often reflecting on the nature of human relationships and the fragility of social bonds.

The narrative explores Shitataka's attempts to understand his situation and find ways to break free from his invisible state. His journey is punctuated by moments of introspection and occasional encounters with individuals who, for brief moments, seem to notice him. These fleeting interactions provide glimpses of hope but also deepen his sense of loneliness when they inevitably fade. The story delves into themes of identity, belonging, and the human need for recognition, as Shitataka grapples with the emotional toll of his condition.

Key characters include Shitataka's classmates, who remain oblivious to his presence, and a few individuals who exhibit subtle awareness of him, such as a teacher who occasionally acknowledges his existence or a classmate who seems to sense his presence without fully understanding it. These characters serve as foils to Shitataka's isolation, highlighting the contrast between his invisible existence and the vibrant, interconnected lives of those around him.

The plot unfolds in a slice-of-life format, with a focus on Shitataka's internal struggles and the quiet, often melancholic moments of his daily routine. The series avoids dramatic confrontations or overt supernatural elements, instead relying on a subdued, introspective tone to convey its themes. Through Shitataka's experiences, the manga examines the complexities of human interaction and the profound impact of being unseen in a world that thrives on connection and recognition.