Taking place in the year 1937 on the eve of World War II, the story involves a mysterious spy training organization known as the "D Agency." The organization is established by Lieutenant Colonel Yuuki from the Imperial Japanese Army. His ideals lead him to recruit people beyond military academy graduates and personnel, while training them to become skilled agents in arts of manipulation. These agents would become a specialized team to conduct operations. One such antihero agent, under the name Jirou Gamou, goes on a harrowing mission to uncover secret documents titled "Black Notes," while battling forces from within and without his own ranks.

Avid bookworm and college student Motosu Urano ends up dying in an unforeseen accident. This came right after the news that she would finally be able to work as a librarian as she had always dreamed of. When she regained consciousness, she was reborn as Main, the daughter of a poor soldier. She was in the town of Ehrenfest, which had a harsh class system. But as long as she had books, she didn't really need anything else. However, books were scarce and belonged only to the nobles. But that doesn't stop her, so she makes a decision... "If there aren't any books, I'll just create some."

17 years ago, immortals first appeared on the battlefields of Africa. Later, rare, unknown new immortal lifeforms began appearing among humans, and they became known as "Ajin" (demi-humans). Just before summer vacation, a Japanese high school student is instantly killed in a traffic accident on his way home from school. However, he is revived, and a price is placed on his head. Thus begins a boy's life on the run from all of humankind.

The Alzano Imperial Magic Academy is located in the southern part of the Alzano Empire and is among most prominent magic schools in the world, where students can learn the highest forms of magic. All those who strive to learn magic dream of studying at this academy, and its students as well as its teachers are proud to be a part of its 400-year history. Glenn Radars is a new instructor who has suddenly been appointed to teach part-time at this highly respected academy. The previously unheard-of lessons of this man known as a good-for-nothing bastard are about to begin.

In a world consisting of numerous isles, a young hero from the Astora Isle encounters the adventurer Kyle and follows him on an expedition on the isle. They meet a mysterious girl named Iris and a talking white cat, and together they make their way to the isle's ruins, where they find a flying island. Kyle becomes consumed by darkness there, and the party resolves to travel to the ends of the world on the flying island in order to find the seven "Great Runes", following Kyle's words before he disappeared.

Follow the intergenerational feud between the Joestar Family and various forces of evil, the most prominent of which is Dio Brando and his followers.