Long ago, a race called the Shadow Angels invaded Earth to harvest the life force of its inhabitants. Due to some outrageous miracle, the Shadow Angels fell dormant, allowing humanity to survive for another 12,000 years without fearing their presence. However, 11 years after a catastrophe known as the Holy Genesis devastated the Earth, the Shadow Angels awoke from their slumber and resumed their attacks. To give humanity a fighting chance, an organization named DEAVA was established, and the use of a robotic weapon called Aquarion was authorized. To bring the Aquarion to full power, three pilots must merge their hearts, bodies, and souls into one—a feat few can hope to achieve. Consequently, the search for so-called 'Element Users' was prioritized, in the hope of securing humanity's future. Sousei no Aquarion follows the story of Apollo, a near-feral young man raised in poverty, who is believed to be a reincarnated legendary hero. After his best friend is taken by the Shadow Angels, Apollo decides to become an Aquarion pilot. Will he be able to turn the tide of the war and free humanity from the threat of the Shadow Angels once and for all?