A cheerful and empty-headed android girl named Honey Kisaragi poses as a high school student while secretly investigating the murder of her father, the scientist Dr. Koshiro Kisaragi. Her primary weapon is the Honey System, also called the Atmospheric Element Condenser, a device implanted in her body that allows her to transform into the red-costumed warrior Cutie Honey by pressing a heart-shaped charm on her necklace and shouting Honey Flash. She is aided in her mission by Seiji Hayami, a bumbling but earnest private detective who lives in a riverside slum and dreams of writing a thesis on the dark underbelly of modern Japan.

Together, they battle Panther Claw, a shadowy criminal organization that profits from human cruelty through deadly gambling rings, weapons trafficking, and bio-terrorism. Unlike its traditional depiction as a secret society, this version of Panther Claw operates more like a collection of quirky, monstrous entrepreneurs, including a genius with split personalities who runs deadly games, a European gentleman with razor blades in his feet, and an old fishwife who conceals a rocket launcher in her stomach.

The conflict expands dramatically when Honey discovers she is not alone. She meets Miki Saotome, a cold and antisocial girl who transforms into the blue-armored Sister Miki but whose flawed powers cause metallic objects to painfully absorb into and extrude from her body. She also encounters Yuki Kenmochi, a gentle and wealthy sheltered girl who transforms into the white-costumed Sister Yuki but develops a merciless personality and an obsessive, romantic crush on Honey. The three are revealed to be artificial creations, androids built by Dr. Kisaragi in failed attempts to recreate a daughter who died. The truth emerges that Miki, discovering that the doctor had killed her original human family to convert her into an android, murdered their creator.

The narrative shifts from episodic adventures against Panther Claw’s grotesque schemes to a darker, serialized drama as the three women confront their shared, tragic origins. Miki eventually sacrifices her life to save Honey from a trap, though she is temporarily revived with a limited lifespan. Later, Honey is seemingly killed by Yuki at the latter’s request, leading to her body being captured and her powers forcibly transferred to Yuki, who is transformed into a destructive being called Sister Yuki Snow White. In the final confrontation, Miki permanently gives up her own life to resurrect Honey, transferring her powers and weapon, the Boomerang Bleu, into her. Honey, now in a new form called Rumble Honey, battles the corrupted Yuki and frees her from the malicious control of the Panther Claw fishwife. Yuki, purified, chooses to disappear, asking Seiji to protect Honey in her stead. The story concludes with Honey continuing to fight against a reformed Panther Claw, now incorporating the combat techniques of her fallen sisters, declaring herself the single Warrior of Love: Cutie Honey.