"Hōkago no Pleiades" centers around a group of schoolgirls who become involved in a magical quest to restore the fragmented pieces of a magical engine, known as the "Engine Fragment," scattered across their world. The story begins when Subaru, a reserved and curious girl, encounters a small, magical creature named Minato. Minato reveals that he is an alien from the Pleiades star cluster and enlists Subaru's help to collect the Engine Fragments, which are essential for repairing his spaceship and returning home. Subaru is soon joined by four other girls—Aoi, Itsuki, Nanako, and Hikaru—each of whom possesses a unique magical ability tied to their personalities and interests.

The girls transform into magical girls using special brooms, which allow them to fly and wield magical powers. Together, they navigate both their ordinary school lives and their extraordinary mission, balancing the challenges of adolescence with the responsibilities of their magical duties. As they search for the Engine Fragments, they encounter various magical phenomena and obstacles, often requiring teamwork and ingenuity to overcome. The fragments are hidden in different locations, sometimes manifesting as surreal, dreamlike landscapes that test the girls' resolve and creativity.

Throughout the series, the characters' relationships and individual struggles are explored. Subaru, initially hesitant and unsure of her place in the group, gradually grows more confident and forms strong bonds with her teammates. Aoi, the most outgoing and energetic of the group, often takes the lead but struggles with feelings of inadequacy. Itsuki, a calm and analytical thinker, provides stability and strategic insight, while Nanako, the youngest and most innocent, brings a sense of wonder and optimism. Hikaru, the most mysterious of the group, harbors a deep connection to the magical world and a personal stake in the mission.

As the story progresses, the girls uncover more about the origins of the Engine Fragments and the true nature of their mission. They learn that the fragments are tied to the balance of their world and that their actions have far-reaching consequences. The narrative builds toward a climactic confrontation, where the girls must confront their fears and doubts to fulfill their mission and protect their world. The series blends elements of magical girl tropes with themes of friendship, self-discovery, and the interplay between the mundane and the extraordinary.