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.

Texhnolyze takes place in the city of Lux, a man-made underground city that has crumbled after years of neglect and lack of repairs. Citizens of Lux have come to refer to their home as simply "The City" and treat it as though it has a mind and will of its own. Three major factions battle to control Lux: Organo, a group of "professionals" who collaborate with the criminal underworld that controls Texhnolyze (prosthetics), the Salvation Union, a populist group that seeks to disrupt Organo's business, and Racan, a collection of young individuals with Texhnolyzes that use their abilities for personal gain. Ichise was once an orphan who has made a place for himself in Lux as a prize fighter. One day, a fight promoter grows angry with him and the altercation that follows results in Ichise losing an arm and a leg. Before death can take him, Ichise is found by the scientist Eriko Kamata, who uses him as a test subject for her newly designed Texhnolyze. With these powerful new limbs at his disposal, Ichise begins to work for Oonishi, the leader of Organo. He soon meets a mysterious young girl, Ran, who has the power to see possible futures. Together, they soon realize that Lux is on the brink of war and collapse, and that they may be the only ones who can save The City.