Set in a distant future where Earth has been abandoned, humanity now inhabits Terra II, a planet colonized by settlers. Due to a genetic anomaly, the population consists solely of men, and reproduction is achieved artificially. The story centers on Otaru Mamiya, a young man living in the nation of Japoness, who stumbles upon three marionettes—advanced humanoid robots with the ability to develop emotions. These marionettes, Lime, Cherry, and Bloodberry, are modeled after the "Maiden Circuit," a rare and advanced AI system that grants them the capacity to grow and learn like humans.

Lime, the first marionette Otaru encounters, is cheerful and energetic, embodying innocence and curiosity. Cherry, the second, is reserved and intellectual, often serving as the voice of reason. Bloodberry, the third, is strong-willed and combative, with a fiery personality. Each marionette represents a distinct aspect of human emotion and behavior, and their interactions with Otaru drive much of the narrative. As they develop deeper emotional bonds with him, they begin to exhibit traits that blur the line between machine and human.

The plot unfolds as Otaru and the marionettes become entangled in a conflict between Japoness and the neighboring nation of Gartland, which seeks to exploit the marionettes for military purposes. Faust, the ruler of Gartland, is a formidable antagonist who commands his own marionettes, designed for combat rather than emotional growth. The series explores themes of identity, humanity, and the ethical implications of artificial intelligence, as Otaru and his companions navigate the challenges posed by their adversaries and their own evolving relationships.

Throughout the series, the marionettes' growth is a central focus, as they grapple with their programming and the emergence of genuine emotions. Their journey is marked by moments of humor, drama, and action, as they strive to protect Otaru and each other while discovering what it means to be "alive." The narrative builds toward a climactic confrontation that tests the limits of their abilities and the strength of their bonds, ultimately raising questions about the nature of humanity and the potential for coexistence between humans and machines.