In a world where a shadowy criminal syndicate known as Panther Claw operates with impunity, a seemingly ditzy and perpetually cheerful high school girl named Honey Kisaragi leads a secret double life. She is an advanced android created by the brilliant Dr. Kisaragi, who implanted her with a miraculous device called the Atmospheric Element Condenser, or the Honey System. By pressing the heart-shaped charm on her necklace and shouting Honey Flash, Honey can solidify the air around her to transform into the powerful, red-clad warrior Cutie Honey. Her abilities are vast, including superhuman strength, intelligence, and the power to create or disperse any object, which she channels through her signature rapier, the Silver Fleuret. Accompanied by her bumbling but kind-hearted friend, a private detective named Seiji Hayami who dreams of documenting the evils of modern Japan, Honey uses her powers to disrupt Panther Claw's operations, unaware of the dark secrets tied to her own creation.

As Honey battles the syndicate's monstrous executives, including the cold-hearted, multi-personality gambler Yuji Nakajo and the hot-tempered gentleman with blade-feet, Duke Watari, she discovers she is not alone. She encounters Miki Saotome, a stoic and deeply troubled loner who possesses the same flashing ability but with a terrible flaw. Whenever Miki transforms into her blue-armored Sister Miki, any nearby metal is painfully absorbed into her body, forcing her to extract it later. Miki carries the additional burden of being the one who murdered Dr. Kisaragi, her own creator, after learning he had inadvertently caused the death of her original family to turn her into an android. Soon after, the wealthy and sheltered Yuki Kenmochi enters the fray. Yuki transforms into the white-clad Sister Yuki, a refined but ruthlessly efficient fighter who harbors a possessive and obsessive romantic love for Honey. All three are revealed to be artificial daughters of Dr. Kisaragi, each a flawed or discarded attempt to recreate a lost child, and their clashing personalities make for an uneasy alliance against Panther Claw.

The narrative arc deepens as the three sisters confront their traumatic origins and the sinister Panther Claw, whose executives include the predatory school principal Mayumi Karasugawa and the seemingly ordinary fishmonger Hiromi Tanaka, who rules her local market with an iron fist and a hidden rocket launcher. The battle takes a tragic turn when Miki sacrifices herself to save Honey, only to be later revived by a reluctant Mayumi with a limited lifespan. As the series hurtles toward its conclusion, Yuki, corrupted by her unrequited love and manipulated by Hiromi Tanaka, ultimately kills Honey. However, Honey is resurrected again when Miki willingly gives up her own life to transfer her powers into Honey's body. In a final confrontation, Honey, now wielding abilities reminiscent of both her fallen sisters, is forced to destroy the brainwashed Yuki. With Panther Claw dismantled and her sisters gone, a now-matured Honey chooses to continue her mission, taking on the mantle of the Warrior of Love as she moves forward, with the spirits of Miki and Yuki living on within her.