Long ago there was a war between the humans and the angels. After the angel Apollonius fell in love with the human Celiane, he tore the wings off of his back and helped humanity by creating the only machine capable of fending off the angels: Aquarion. He was eventually defeated by one of his comrades. Twelve thousand years later, the angels have returned to once more take the life-force of all humans. Aquarion's whereabouts are unknown, but humanity is fighting its hardest until the keys to victory can be found. In order to defeat the angels they need the aid of Aquarion and the re-incarnations of the lovers that saved humanity before, Celiane and Apollonius.