"Cutey Honey" centers on Honey Kisaragi, a high school girl who is actually an advanced android created by Dr. Kisaragi. Honey possesses the ability to transform into various forms, each with unique abilities, using the "Airborne Element Fixing Device." This technology allows her to alter her molecular structure, granting her superhuman powers to combat evil. The narrative unfolds as Honey battles the Panther Claw organization, a sinister group led by Sister Jill, who seeks to conquer the world through chaos and destruction.

Panther Claw employs a series of powerful and often grotesque monsters, known as Panther Zoku, to carry out their plans. Honey's transformations, referred to as "Honey Flash," enable her to adapt to different combat scenarios, making her a formidable opponent. Throughout the series, Honey's missions involve thwarting Panther Claw's schemes, rescuing innocent people, and uncovering the truth about her own origins. Her journey is marked by a blend of action, humor, and moments of introspection as she grapples with her identity as an android and her role as a protector of justice.

Supporting characters include Honey's allies, such as her adoptive father figure, Inspector Genjiro Todoroki, and his assistant, Seiji Hayami. These characters provide both strategic assistance and emotional support, contributing to the series' dynamic. The interplay between Honey's dual life as a student and a superhero adds depth to her character, highlighting themes of duty, identity, and the struggle between good and evil.

The series is structured around episodic confrontations with Panther Claw, each episode presenting a new threat that Honey must overcome. Despite the episodic format, there is an overarching narrative that gradually reveals more about Panther Claw's ultimate goals and Honey's connection to them. The climax of the series involves a direct confrontation between Honey and Sister Jill, leading to a resolution that ties together the various threads of the story.

"Cutey Honey" is notable for its pioneering role in the magical girl genre, blending elements of science fiction, action, and comedy. The series' innovative use of transformation sequences and its focus on a strong, independent female protagonist have left a lasting impact on the genre. The narrative's balance of lighthearted moments and intense action sequences ensures a compelling viewing experience, making it a significant entry in the history of anime.