Rail Wars! is set in an alternate universe where the Japanese government retains control over the nation's railway systems. Due to the stability provided by government leadership, the railway network is permitted to thrive. Naoto Takayama aims to become an employee of Japan National Railways because of the comfortable lifestyle it would allow him to lead. To achieve this, he joins its training program, where students must prove their knowledge of trains as well as their readiness for any challenge that might arise. During this period, he meets other students, including the athletically gifted Aoi Sakura, the perpetually hungry Sho Iwaizumi, and the human encyclopedia Haruka Komi. Together, they strive to survive their trainee period while dealing with purse snatchers, bomb threats, and the looming presence of the extremist “RJ” group, which seeks to privatize the railway system.