12,000 years after the war against the Shadow Angels, Amata Sora spends his days working in a movie theater until he meets and befriends a girl his age named Mikono Suzushiro. When a mysterious invading force, known as "Abductors" from the planet Altair and led by Kagura Demuri, attacks, Amata and Mikono find themselves in danger, until Amata activates his hidden levitation power and unlocks the sealed power of Aquarion to form Aquarion Evol.