In the near future, Earth faces a catastrophic threat from mysterious biomechanical creatures known as WORMs, which emerge from the ocean and wreak havoc on humanity. In response, the global military develops advanced powered exoskeletons called Sonic Diver units to combat the invaders. However, traditional pilots struggle to operate these machines effectively due to their high physical demands. To address this, a new program is initiated, recruiting young girls with exceptional physical and mental capabilities to pilot specialized Sonic Diver units. These girls form the Sky Girls, an elite squadron tasked with defending the planet.

The story centers on three main characters: Eika Ichijo, a disciplined and skilled pilot with a strong sense of duty; Otoha Sakimori, a cheerful and optimistic girl who joins the team to protect her loved ones; and Karen Shishidou, a reserved and analytical prodigy with a deep understanding of technology. Together, they undergo rigorous training and form a close bond as they prepare to face the WORMs. The narrative explores their personal struggles, growth, and camaraderie as they confront both external threats and internal challenges, such as the ethical implications of using young pilots in warfare.

As the Sky Girls engage in battles against the WORMs, they uncover deeper mysteries about the origins of the creatures and the true purpose of their mission. The series balances action-packed combat sequences with moments of character development, highlighting the emotional and psychological toll of war on the young pilots. Themes of sacrifice, resilience, and the importance of teamwork are woven throughout the story, creating a compelling blend of science fiction and human drama. The series concludes with a climactic confrontation that tests the limits of the Sky Girls' abilities and resolve, leaving a lasting impact on their lives and the world they fight to protect.