"Comet-san" centers on the life of a young girl named Comet, who lives in a small, rural town. The narrative explores her daily experiences, relationships, and personal growth as she navigates the challenges of adolescence. Comet is depicted as a kind-hearted and curious individual, often finding herself in situations that highlight her resilience and empathy. Her interactions with family, friends, and townspeople form the core of the story, offering a slice-of-life portrayal of her world.

The plot unfolds through a series of episodic vignettes, each focusing on different aspects of Comet's life. These include her school life, where she deals with typical teenage concerns such as friendships, academic pressures, and self-discovery. Her family dynamics are also a significant element, particularly her relationship with her parents and younger sibling, which is portrayed with warmth and occasional tension. The manga delves into themes of community, as Comet often engages with the townspeople, participating in local events and helping others in need.

Supporting characters play crucial roles in shaping Comet's journey. Her best friend, a spirited and outgoing girl, provides a contrast to Comet's more reserved nature, often encouraging her to step out of her comfort zone. A local shopkeeper, who serves as a mentor figure, offers wisdom and guidance, helping Comet navigate her challenges. The narrative also introduces a love interest, a boy from her school, whose interactions with Comet add a layer of romantic tension and exploration of young love.

The setting of the rural town is integral to the story, with its serene landscapes and close-knit community providing a backdrop that enhances the themes of simplicity and connection. The changing seasons are often used to reflect Comet's emotional states and the passage of time, adding depth to the storytelling.

Throughout the series, "Comet-san" balances moments of humor, tenderness, and introspection, creating a well-rounded portrayal of its protagonist's life. The manga's episodic structure allows for a gradual unfolding of Comet's character, making her growth and experiences relatable and engaging. The narrative avoids heavy drama, instead focusing on the quiet, everyday moments that shape Comet's world and her understanding of herself and those around her.