With Rabbi Village greatly expanding under the management of his subordinates Isami Tahara and Yuu Kirino, Hakuto Kunai can now resume his adventures while looking for items to counteract magic. He begins his search at the Prison Labyrinth in Rookie Town, where a secret laboratory deep within the dungeon gives him insight into technology that is far more advanced and dangerous than anything in the rest of the world. Meanwhile, Rabbi Village has gained unwanted international attention from the newly formed Queendom of Xenobia, which wishes to drive a wedge between the Holy Kingdom of Light and the State of Right. But with Kunai's newly summoned aide, Akane Fujisaki, at his disposal, things may not go as the Queendom plans.

Despite Kyouko Honda's tragic death, her vivid memory lives on, providing guidance through times of hardship to her close ones. However, Kyouko was not always the wise and radiant person that she is fondly remembered as in the present day. Feeling deserted by her own family and rejected by society, a young Kyouko abandons stability for a life of delinquency, jeopardizing her education and future. Fortunately, her descent into despair is interrupted by a fateful encounter with her husband-to-be Katsuya, who has recently started his teaching internship at her school. With a composure surprisingly unaffected by Kyouko's tantrums, Katsuya quickly wins her over through his gentleness and attention toward her—sincere gestures that she has never received before. As the two grow closer together, Kyouko opens her tormented heart to him and, along with it, a door to new horizons.

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.

In a world where humans coexist with androids called Neans, a group known as the Immortal Nine rises up against society. Tasked with disposing of the revolters, a Nean named Rouge Redstar (aka Metal Rouge) and investigator Naomi Orthmann head to Mars to track them down…but first, Rouge wants some chocolate.