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.

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.

"Stride"—an extreme sport that combines parkour, free running, relay, and sprinting—is what made first year high school student Nana Sakurai enroll in Honan Academy, after being captivated by the school's stride team. Sharing the mutual intention of joining the team is fellow first year and stride maniac, Takeru Fujiwara, and together they request to join. Much to their dismay, however, the stride club is no longer active due to lack of members, and they are now operating under the shogi club. In order to revive the stride club, Nana and Takeru recruit first year Riku Yagami—a fast runner who is interested in almost every sport. With this new team, the club now aims high at a new goal: to win the prestigious End of Summer competition, and bring the Honan stride team back to their prime.

In an ordinary town, there are people who live a peaceful and fulfilling life. But they don't know that it is a false peace. The untold truth... The earth has already been destroyed... 99.9% of the human race has been wiped out by a mysterious alien force from outer space. The enemy is named "Dracters." Eventually, a large hole was drilled in the earth and terraformed into a suitable environment for the aliens to live. Humans have no choice but to hide in shelters to escape their eyes. Waiting for the day of resurrection, which they do not know when it will come... The inhabitants of the shelter Ixia have had their memories of the day of destruction erased, and live a normal life without knowing anything about it. However, some of them, the "chosen ones," have become pilots, driving giant robots called "Rogue" and fighting against aliens. Today, another new pilot is selected...