"Hōkago no Pleiades" centers on a group of schoolgirls who join an after-school astronomy club, only to discover that the club is a front for a magical mission to recover fragments of a broken engine from a spaceship. The engine, belonging to an alien named Subaru, was shattered and scattered across Earth, causing disruptions in gravity and other natural phenomena. The girls are chosen by miniature alien beings called the Pleiadian Envoys, who grant them magical powers and transform them into magical girls. Each girl wields a unique wand that allows them to fly and manipulate gravity, aiding in their quest to locate and retrieve the engine fragments.

The protagonist, Aoi Aoki, is a cheerful and determined girl who becomes the leader of the group. Her friends include Subaru, a mysterious transfer student who is revealed to be the alien whose engine was destroyed; Itsuki, a shy and reserved girl with a strong sense of responsibility; Nanako, a bubbly and energetic character who often provides comic relief; and Hikaru, a mature and level-headed member who balances the group dynamics. Together, they navigate the challenges of balancing their magical duties with their everyday school lives, all while uncovering the truth behind Subaru's past and the purpose of the Pleiadian Envoys.

As the story progresses, the girls face increasingly difficult trials, including encounters with gravity anomalies, rival magical entities, and internal conflicts within the group. The narrative explores themes of friendship, perseverance, and the consequences of tampering with advanced technology. The climax involves a confrontation with a powerful antagonist who seeks to exploit the engine fragments for their own gain, forcing the girls to confront their fears and unite to protect Earth and restore Subaru's engine. The series concludes with the resolution of their mission, though it leaves room for reflection on the bonds they have formed and the impact of their extraordinary experiences on their lives.