"Erementar Gerad - Flag of Blue Sky" is a manga series set in a world where sentient weapons known as Edel Raids exist. These weapons can transform into human forms and bond with humans to unlock their full potential. The story centers on Cou, a young sky pirate who stumbles upon Ren, an Edel Raid in the form of a girl. Ren is highly sought after due to her immense power and the mysterious "Grand Shard" embedded within her, which is said to grant immense power to those who possess it.

Cou and Ren form a bond, and Cou becomes her "Waver," the human partner who can wield her power. Together, they embark on a journey to uncover the secrets of the Grand Shard and Ren's origins. Along the way, they encounter various factions, including other sky pirates, military organizations, and rogue Edel Raids, all vying for control of Ren and the Grand Shard. The narrative explores themes of trust, identity, and the consequences of wielding power, as Cou and Ren navigate a world filled with danger and intrigue.

The series features a diverse cast of characters, including Cisqua, a skilled sky pirate and Cou's childhood friend, and Kuea, a mysterious and powerful Edel Raid with her own agenda. The interactions between the characters drive the plot forward, as alliances are formed and tested, and the true nature of the Edel Raids and the Grand Shard is gradually revealed. The story balances action-packed sequences with moments of introspection, delving into the emotional and psychological struggles of the characters as they confront their pasts and the challenges ahead.