"Hōkago no Pleiades" centers on a group of schoolgirls who join a magical astronomy club to recover fragments of an engine that powers interstellar travel. The fragments, scattered across Earth, are essential for an alien named Subaru to return to his home planet. The girls—Aoi, Itsuki, Nanako, and Hikaru—are chosen by miniature alien beings called the Pleiadian Envoys, who grant them magical abilities and brooms that allow them to fly. Together, they transform into magical girls to locate and retrieve the engine fragments, which are hidden in various locations and guarded by mysterious entities.

The narrative explores the girls' personal struggles and growth as they balance their magical duties with everyday school life. Aoi, the protagonist, is initially hesitant and unsure of her abilities but gradually gains confidence through her experiences. Itsuki is cheerful and optimistic, often serving as the emotional anchor for the group. Nanako is reserved and intellectual, providing strategic insights, while Hikaru is energetic and impulsive, adding a dynamic element to the team. Subaru, the alien they aim to help, remains enigmatic, with his true motives and past gradually revealed as the story progresses.

The series blends slice-of-life elements with magical girl and science fiction themes, creating a unique narrative structure. The girls' missions to recover the fragments are interspersed with moments of camaraderie, humor, and introspection, highlighting their evolving friendships and individual challenges. As they uncover more fragments, they also learn about the broader implications of their mission, including the connection between the engine fragments and the fabric of space-time. The story culminates in a climactic confrontation that tests their resolve and unity, ultimately resolving the central conflict while leaving room for reflection on their journey.