"Kotaro Lives Alone" centers on Kotaro Sato, a four-year-old boy who moves into an apartment complex by himself. Despite his young age, Kotaro exhibits remarkable independence, handling daily tasks such as cooking, cleaning, and budgeting with surprising competence. His mature demeanor and polite speech contrast sharply with his childlike appearance, creating a poignant dynamic that drives the narrative. The series explores Kotaro's interactions with his neighbors, particularly Shin Karino, a struggling manga artist who becomes an unlikely caretaker and friend. Through their evolving relationship, the story delves into themes of loneliness, resilience, and the importance of community.

Kotaro's backstory is gradually revealed, shedding light on the circumstances that led to his solitary living situation. His past is marked by hardship, including neglect and abandonment, which explains his self-reliance and emotional guardedness. Despite these challenges, Kotaro maintains a cheerful and optimistic outlook, often inspiring those around him. The series balances moments of humor and warmth with deeper, more somber reflections on societal issues such as child welfare and the struggles of single parenthood.

The supporting cast includes other residents of the apartment complex, each with their own struggles and stories. Mizuki Akitatsu, a former child actor, and Tamaru, a yakuza member with a soft spot for Kotaro, provide additional layers to the narrative. Their interactions with Kotaro highlight the impact of his presence on their lives, as they find themselves drawn to his innocence and determination. The series avoids overt melodrama, instead opting for a grounded and empathetic portrayal of its characters and their interconnected lives.

Through its episodic structure, "Kotaro Lives Alone" weaves together moments of everyday life with gradual revelations about Kotaro's past and the challenges faced by those around him. The narrative emphasizes the importance of human connection and the ways in which even the smallest acts of kindness can have a profound impact. By focusing on Kotaro's resilience and the relationships he forms, the series offers a heartfelt exploration of themes relevant to both children and adults.