In a distant future, humanity is once again facing the threat of the "Shadow Angels," mystical creatures who have returned after 12,000 years of absence. They attack human cities and kidnap their inhabitants in order to drain their "prana" (vital energy). To fight against them, youngsters with special powers from around the world were gathered and trained to pilot the "vector machines," three ancient ships that together form mankind's ultimate weapon, "Aquarion." The story revolves mainly around Apollo, a teenager rumored to be the reincarnation of Apolonius, a fallen angel who fought against his own kind to protect mankind.