Set in a distant future where Earth has become uninhabitable, humanity has colonized a new planet named Terra II. Due to a catastrophic event during colonization, the population consists solely of men, with no women remaining. To compensate, advanced androids called Marionettes are created to serve as companions and laborers. These Marionettes lack emotions and are purely functional, but a unique type called Saber Marionettes is developed with the potential to possess human-like emotions and personalities.

The story centers on Otaru Mamiya, a young man living in the nation of Japoness. Otaru stumbles upon Lime, Cherry, and Bloodberry, three Saber Marionettes who have developed emotions due to a rare phenomenon known as the "Maiden Circuit." Each Marionette exhibits distinct personalities: Lime is cheerful and energetic, Cherry is shy and reserved, and Bloodberry is bold and assertive. Otaru forms a close bond with them, and together they navigate various challenges, including protecting Japoness from external threats and uncovering the mysteries surrounding the Maiden Circuits.

A significant antagonist is Faust, a powerful and enigmatic figure who seeks to control the Saber Marionettes for his own purposes. Faust’s ambitions often bring him into conflict with Otaru and his companions, leading to intense battles and moral dilemmas. The narrative explores themes of humanity, identity, and the nature of emotions, as the Marionettes grapple with their newfound feelings and their place in a world dominated by men.

The series also delves into the origins of the Maiden Circuits and their connection to the lost history of Terra II. As Otaru and the Marionettes uncover more about their world, they encounter other nations and factions, each with their own agendas and perspectives on the role of Marionettes. The interplay between technology and humanity is a recurring motif, as the characters question what it means to be truly human in a world where artificial beings can experience emotions.

Throughout the series, the relationships between Otaru and the Marionettes evolve, with moments of camaraderie, conflict, and growth. The narrative balances action, humor, and emotional depth, creating a story that is both engaging and thought-provoking. The series concludes with resolutions to key conflicts, though it leaves room for reflection on the broader implications of its themes.