Long ago, a goddess descended from Heaven and blessed the desolate land of Gatepia. As a result, gigantic gates appeared, leading to dungeons abundant in "kirakuri," crystals containing the energy needed for the foundation of the world. This led to the formation of various companies of adventurers who would harvest kirakuri from the dungeons. Following his father's disappearance inside one of the biggest gates in Gatepia, Minato is urged by his childhood friend Yutoria to become the president of his father's treasure-hunting company—the Kibou Company. He reluctantly agrees and meets with the other employees: the priest Makoto, the soldier Akari, and the accountant Guide. Thus, Makoto begins his tenure as president. As he and his comrades strive to fulfill various missions and other assorted tasks in order to keep their small company alive, they will uncover the mystery behind their former leader's sudden departure.

Rail Wars! takes place in an alternate universe where the Japanese government remains in control of the nation's railway systems. Because of the stability afforded by the leadership of the government, the railway system is allowed to flourish. Naoto Takayama aspires to become an employee for Japan National Railways because of the comfortable life that it will enable him to live. In order to accomplish this he enters its training program, where students must demonstrate their knowledge of trains as well as their ability to be ready for any challenge that might arise. During this time period he will encounter other students such as the athletically gifted Aoi Sakura, the constantly hungry Sho Iwaizumi, and the human encyclopedia Haruka Komi. Together they will work towards surviving their trainee period, all the while taking on purse snatchers, bomb threats, and the looming specter of the extremist “RJ” group who wants to privatize the railway system.

After fending off the threat of a Neuroi invasion of Romagna and destroying the enemy's nest over Venezia, Yoshika Miyafuji goes back to her home town in the Empire of Fusou. Despite the loss of her magical and healing abilities, the former officer of the 501st Joint Fighter Wing wants to continue studying medicine. This is in order to help those in need, both civilians and those on the front lines alike. She receives an invitation from a prestigious school in Europe and decides to accept the offer, embarking on a journey back to the war-torn continent. However, a new danger arises, as more and more Neuroi manage to break through human defense lines, appearing unnoticed in supposedly safe areas and disturbing the balance of power in Europe. Yoshiki's sense of duty collides with her inability to pilot a Striker Unit, but with her friends in peril, it seems that there is only one thing she can do.

Cyberpunk: Edgerunners tells a standalone story about a street kid trying to survive in a technology and body modification-obsessed city of the future. Having everything to lose, he chooses to stay alive by becoming an edgerunner—a mercenary outlaw also known as a cyberpunk.