Human race had lost 2/3 of the world’s population because of a random act of nature. The ice on the Antarctica melted, and Atlantis appeared. It was the civilization ruined 12,000 years ago. Because of this, the Fallen Angels got revived. They were a race of humans with wings and they sent biomechanical weapons called “Mythical Beasts” into cities to capture people in order to drain them of biological energy called “Purana”. The human were excavating the ruins on the bottom of the sea to look for fighter planes, “Vector Machines”. They were the weapon that was said to run the Fallen Angels. Vector Machines combine together and turn into “Machine Angel Aquerion”. In order to operate Aquerion, a person with the Element ability only could be compatible with the system; they gathered teenagers for candidates to be pilots. Then, the day came when “Machine Angel Aquerion” appeared.
The story revolves mainly arround Apollo, a teenager rumored as the reencarnation of Apollonius, a fallen angel who fought against his own kind to protect mankind. Few believe it could be true, but the fact is that dispite his untamed and reckless nature, he proved to be an invaluable asset in Aquarion's battle against mankind's sworn enemy, which resumed recently, after a 12.000 year hiatus.