"Clean-Freak Fully-Equipped" centers on Aoyama, a high school student with an obsessive-compulsive disorder (OCD) related to cleanliness. His condition manifests in an extreme aversion to dirt and germs, leading him to carry a fully-equipped cleaning kit at all times. This compulsion complicates his daily life, particularly when he encounters messy or chaotic situations. Despite his struggles, Aoyama is determined to live a normal life and forms meaningful connections with those around him.

The narrative explores Aoyama's interactions with his classmates, particularly Asako, a carefree and messy girl who becomes a central figure in his life. Their contrasting personalities create both comedic and heartfelt moments as Aoyama navigates his discomfort with her untidiness while gradually developing a deeper bond. The story also delves into Aoyama's past, revealing the origins of his OCD and how it has shaped his worldview. Through his relationships and experiences, Aoyama begins to confront his fears and learns to manage his condition in a way that allows him to grow emotionally.

The manga balances humor and introspection, using Aoyama's cleaning rituals as a metaphor for his internal struggles. Themes of acceptance, personal growth, and the importance of human connection are woven throughout the narrative. Supporting characters, such as Aoyama's classmates and family members, provide additional layers to the story, highlighting how his condition impacts those around him and how they, in turn, influence his journey. The series maintains a lighthearted tone while addressing the challenges of living with OCD, offering a nuanced portrayal of mental health and resilience.