Long ago, a race called the Shadow Angels attacked Earth to drain the life force from everyone living there. Through an extraordinary miracle, the Shadow Angels fell into dormancy, allowing humanity to survive for another 12,000 years without fear of them. However, 11 years after a catastrophe known as the Holy Genesis devastated the planet, the Shadow Angels awakened and resumed their assaults.
To give humanity a fighting chance, an organization named DEAVA was established, and a robotic weapon called Aquarion was deployed. To unlock Aquarion's full potential, three pilots must unite their hearts, bodies, and souls—a feat only a rare few can achieve. Consequently, the search for so-called 'Element Users' became a priority, in hopes of securing humanity's future.
Sousei no Aquarion follows the story of Apollo, a nearly feral young man raised in poverty, believed to be the reincarnation of a legendary hero. After his best friend is taken by the Shadow Angels, Apollo decides to become an Aquarion pilot. Can he turn the tide of the war and free humanity from the Shadow Angels' threat once and for all?