"Saber Marionette J" is set in a distant future where Earth has become uninhabitable, leading humanity to colonize a new planet named Terra II. Due to a catastrophic event during colonization, the planet's population consists solely of men, as all women perished. To compensate for the absence of women, advanced humanoid robots called "Marionettes" were created to assist with daily tasks. These Marionettes lack emotions and are purely functional.

The story centers on Otaru Mamiya, a young man living in the nation of Japoness. One day, Otaru discovers three unique Marionettes—Lime, Cherry, and Bloodberry—who possess the rare ability to experience emotions, a trait known as the "Maiden Circuit." These Marionettes were originally part of a failed military project, but Otaru forms a bond with them, treating them as individuals rather than mere machines. Lime, the cheerful and energetic one, Cherry, the gentle and nurturing type, and Bloodberry, the fierce and combative, each bring distinct personalities to the group.

As Otaru and the Marionettes navigate their lives, they encounter Faust, a rogue scientist who seeks to exploit the Maiden Circuit for his own ambitions. Faust creates his own Marionettes, including the powerful and emotionless Panther, to challenge Otaru and his companions. The conflict escalates as Faust's plans threaten the stability of Japoness and the lives of its inhabitants.

Throughout the series, themes of humanity, emotion, and the ethical implications of artificial intelligence are explored. The Marionettes' growing emotional capacities challenge the societal norms of Terra II, where they are traditionally seen as tools. Otaru's relationships with Lime, Cherry, and Bloodberry evolve, highlighting the complexities of their existence as sentient beings.

The narrative combines action, humor, and heartfelt moments, with battles between Marionettes showcasing their unique abilities and personalities. The story delves into the origins of the Maiden Circuit and the broader implications of creating life-like androids capable of emotions. As the series progresses, the characters confront their identities and the moral dilemmas surrounding their creation, culminating in a climactic struggle to protect their world and define their place within it.