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?

The Nocturnal Community Relations Division is a team of people who specialize in solving cases involving the ominous occult creatures of the night unseen by ordinary humans. Young and unsuspecting Arata Miyako has been assigned to the Shinjuku Ward Office of the division, where he meets his fellow members Theo Himezuka and Kyouichi Sakaki. On his first night, Arata finds himself on a mission where he discovers to his surprise that not only does every supernatural creature he once thought to be fictional actually exist, but also that he is the only human who can understand their non-human speech. Arata's surprises do not end there, as later that night, he meets a legendary creature called a Tengu that refers to him as the famous Heian-era exorcist, Abe no Seimei. Unfamiliar with the exorcist, Arata pays no mind and continues to work with his team, utilizing his unique ability to assist in the resolution of their cases. Mistaken by many occult creatures as Abe no Seimei and quickly becoming notorious for his special ability during his work, Arata becomes curious of his origins and invests himself more into solving cases regarding occult creatures he encounters once he learns of a certain connection between himself and the exorcist. However, Arata will quickly find that dealing with supernatural creatures is not as simple as he thought, as danger begins to play a fundamental role in his everyday findings and his ability starts to present an unexpected issue.

Shout and Crunchy are "trash throw away-ers" who work in the dead of night. Makina is a 16-year-old witch who has come to the world of humans and to London to study for one year about how to become a proper bride. But Makina searches for Shout and Crunchy, and begs them to throw away her "Witch's Book." Truthfully, Makina wants to quit being a witch and become a normal girl, and the book is just a hindrance. But the book is not something one can simply just throw away.

Marion is a young schoolboy who prides himself on his adherence to a philosophy he calls "rationalism". Because of his disdain for emotional display, he ignores anything remotely akin to affection. But when he's entangled in a romantic affair with an older courtesan, his rationalism is revealed to be little more than a cover for his own emotional immaturity. Learning to love, Marion blossoms under his older lover's care but unfortunately, Marion has yet to learn the true price of the affair.