In a distant future, humanity once again is facing the threat of the "Shadow Angels". Mystical creatures who 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 arround 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 arround Apollo, a teenager rumored as the reencarnation of Apolonius, 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 the battle against the Shadow Angels.
Ikuto Touhouin is a young boy that was thrown out to sea when he was onboard a ship and there was a vicious storm. When he comes to, he discovers himself on an island named Airantou. As he wanders the grounds he notices that something is strange... but not much thought is put into it since girls (lots of them) crazily chase him 'round the island.Ikuto searches for an escape and starts heading out of the island by boat, however, the island is surrounded by whirlpools that will definitely kill. Finally admitting that he won't be able to leave the island alone, he decides to settle down.... and that's when he finds out that the island is only inhabited by women.