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?

Shun Asanaga is a 15-year-old junior high school student with an optimistic and bright personality. One day, he finds a mysterious crystal in the office of his father, who is a scientist and businessman. When Shun touches it, the world becomes distorted, and he is sent into the world of Endra. Emilio, a prince of the kingdom of Endra, is nearing his 16th birthday and despises the reigning king, Delzain. Since Emilio is now at the age when he can inherit the throne, he takes up a weapon and attempts revenge. However, because Emilio is too weak, he is captured by Delzain and put in prison. When Emilio is in grief, the wall of his cell becomes distorted and Shun appears from there with two goals: return to his own world, and complete Emilio's revenge. What future lies ahead for the two boys trying to survive in Endra, yet raised in two different worlds?

Long ago, the king of Orvelia, Kyle, defeated the demon king Angmund and brought peace to the world. However, one hundred years later, demons have been sighted in the forests, threatening humanity once more. A scouting expedition is sent to verify the claim but only one member returns. Meanwhile, Riheet, the leader of a dark elf mercenary group, plots to take over Orvelia to exact revenge against the humans who forsook their race a century ago. The knight apprentice Kasel, accompanied by the priestess Frey, sets out to rescue Clause, an old friend who went missing in the tragic mission. However, along the way, Kasel discovers that he is the son of the revered King Kyle and the only one who can wield the Holy Sword Aea—the same sword that slew the demon king. To fulfill this destiny, the young knight must embark on a perilous quest, unseal the sword, and end the fear instilled by demons. As Kasel's journey to bring hope to humanity and Riheet's vow for vengeance intertwine, what fate could possibly await them?

After being brutally murdered along with her family, Makina Hoshimura turns into a Shikabane Hime, a living corpse contracted to the Kougon Cult, in order to exert revenge on the mysterious undead organization responsible for her death. She is assisted in this task by Keisei Tagami, her contracted priest and former friend. This series follows the story of Keisei's younger brother Ouri, a boy with an unusual attraction to death, who slowly discovers his brother's secret and gets dragged into the world of the Shikabanes.