Honey Kisaragi is a regular Catholic schoolgirl, until the day her father is murdered by the "Panther Claw" organization. After his death, she learns she is actually an android created by him and within her is a device that can "create matter from the air". With her cry of "Honey Flash!" she can use the device to transform into the sword-wielding red-haired superhero, Cutie Honey.
While attending the Saint Chapel School for Girls, Honey seeks revenge against the Panther Claw, which is ruled by Panther Zora and her younger sibling Sister Jill. Zora wants "the rarest items in the world" and seeks Honey's device, while Jill, leader of the group's division in Japan, "only wants the finest riches" and has a crush on Honey.
Honey is aided in her quest by Danbei Hayami and his two sons, journalist Seiji and young Junpei.