Humanity is once again in danger from mystical creatures called Shadow Angels, that have not been seen in over twelve thousand years. The Shadow Angels attack human cities and use the human inhabitants to drain their vital energy, also known as prana.
The only people who can fight these beings are teenagers known as Elements. They are the only one capable of piloting the three ancient "Vector" ships, and together they form the "Aquarion" unit.
The story focuses mainly on one of these Elements, Apollo. He is said to be the reincarnation of the Shadow Angel Apolonius, who fought against its own kin to protect humans a long time ago. Few believe this, however, as he is quite reckless and untamed.