In an alternate reality where Cutie Honey exists only as a fictional television series, a high school student named Yuuta is an ardent fan of the iconic heroine. His devotion to the character is so consuming that it inadvertently distracts him from acknowledging the obvious affection of his childhood friend and next-door neighbor, Midori.

Yuuta's life takes an unexpected turn when a mysterious humanoid alien girl crash-lands near his home. The girl has no memory of her past and possesses a naive, innocent personality, easily fascinated by everything she encounters on Earth. When Yuuta takes her in, she becomes deeply intrigued by his extensive collection of Cutie Honey media, quickly learning to emulate the character. Seeing the resemblance, Yuuta decides to name her Honey Kisaragi, the same as his beloved fictional heroine. He initially attempts to keep her existence a secret, but when that proves impossible, he introduces her to the world as a distant cousin.

As Honey spends time in the human world, she discovers she can manifest superhuman powers identical to the fictional Cutie Honey, using them instinctively to protect Yuuta and his loved ones from various threats. These dangers range from mundane human predators to more ominous forces that seem to be pursuing her from beyond the stars. The early narrative establishes a harem-style dynamic around Yuuta, featuring not only the alien Honey and his neighbor Midori but also his teachers, his younger sister, and the actress who plays Cutie Honey in the television series he adores.