"Aquarion Evol" is a science fiction manga series that serves as a sequel to the original "Genesis of Aquarion" story, set 12,000 years after the events of its predecessor. The narrative unfolds in a world where humanity is divided into two factions: the surface-dwelling humans and the subterranean Altairians, who live in the underground city of Vega. The Altairians, led by the enigmatic Mykage, seek to reclaim the surface world, which they believe rightfully belongs to them. To achieve this, they deploy powerful mechanical beings called Abductors to capture humans and drain their life force, known as "prana."

The story centers on Amata Sora, a young man with the unique ability to fly, a trait considered impossible in this world. Amata's life changes when he encounters Mikono Suzushiro, a girl who bears a striking resemblance to a figure from his dreams. Together, they are drawn into the conflict between the surface and Altair when they are recruited by Neo-DEAVA, an organization dedicated to defending humanity. Neo-DEAVA pilots giant mechas called Aquaria, which are formed by combining three smaller vehicles. These mechas are powered by the emotional and spiritual energy of their pilots, emphasizing the theme of human connection and unity.

As the story progresses, Amata and Mikono, along with other pilots such as Zessica Wong and Cayenne Suzushiro, face numerous challenges both on and off the battlefield. The relationship between Amata and Mikono becomes a focal point, as their bond is tested by external forces and internal doubts. Meanwhile, Mykage manipulates events from the shadows, using his agents, including the mysterious Kagura Demuri, to further his agenda. Kagura, who shares a deep connection with Amata, becomes a rival and a key figure in the unfolding conflict.

The narrative explores themes of reincarnation, destiny, and the cyclical nature of history, as characters grapple with their past lives and the roles they are fated to play. The concept of "Vector Machines," ancient relics tied to the original Aquarion, plays a significant role in the story, as they hold the key to unlocking humanity's potential and resolving the conflict between the two factions. The series builds toward a climactic confrontation that ties together the fates of its characters and the legacy of the Aquarion, blending action, romance, and philosophical undertones.