Once upon a time, a race known as the Shadow Angels attacked Earth to harvest the life force of all those who inhabited the planet. Thanks to some outrageous miracle, the Shadow Angels went dormant, and humanity was able to live another 12,000 years without fearing their presence. But 11 years after a catastrophe dubbed the Holy Genesis brought ruin to the Earth, the Shadow Angels were stirred from their slumber and resumed the attacks once more. To give humanity somewhat of a chance, an organization known as DEAVA was formed, and use of a robotic weapon named Aquarion has been authorized. In order for the Aquarion to be brought to full power, three pilots must combine their hearts, bodies, and souls into one—a feat few can hope to accomplish. Thus, the search for so-called 'Element Users' was prioritised, hoping to ensure humanity's future. Sousei no Aquarion follows the story of Apollo, a near-feral young man brought up in poverty, who is believed to be a legendary hero reincarnated. After his best friend is taken by the Shadow Angels, Apollo chooses to become an Aquarion pilot. Will he be able to turn the tides of the war, and free humanity from the threat of the Shadow Angels for once and for all?

Count D, a quite interesting pet shop owner from an area called Chinatown, sells rare and hard to come by pets to people longing for something special, but with each sale comes a contract. If the rules of the contract are followed, everything goes fine, but if someone should break the rules of the contract, the pet shop cannot be held responsible for anything unfortunate that might happen. Leon Orcot, a homicide detective, has linked many odd and unexplainable deaths together; they all were customers of Count D's pet shop, and he intends to find out why.

Lime, Cherry, and Bloodberry, female-like androids called marionettes, have returned to Otaru`s side. The somewhat reformed marionettes of Faust (Tiger, Luchs, and Panther) are sent to stay with Otaru and friends to learn more about being human. Enter a seventh marionette named Marine, who has a mysterious power -- and they all possess the special maiden circuit that allows a marionette to feel emotions!

Kaminashi Nozomi (17) is an exceptional gymnast. So much so that colleges with some of the best gymnastic programs are trying to recruit her. Unfortunately for them, she has other plans. Due to her family being extremely poor, money is everything to her. That's why she wants to step into the world of "Keijo." "Keijo" is a type of gambling sport where girls stand on a small floating platform and compete against one another. The aim is to push the other contestant off of the platform into the water, but they are only allowed to use their butt or breasts to push the others off. Will Nozomi be able to compete in the intense world of "Keijo" and bring wealth and fortune for her family?