Set in an alternate universe, Rail Wars! unveils a realm in which the Japanese authorities supervise and manage the country's railway infrastructure, resulting in a highly efficient and thriving transportation network. Naoto Takayama yearns for a hassle-free existence as a member of Japan National Railways and enrolls in the establishment's training course to pursue his aspirations. As part of the program, learners gain mastery in train operations and acquire the ability to handle challenging scenarios such as obstructing theft, dealing with bomb threats, and countering the anti-government RJ group against rail ownership. Naoto's path crosses with other trainees like the athletic Aoi Sakura, the perpetually famished Sho Iwaizumi, and the erudite Haruka Komi, who all encounter roadblocks together during their training ventures.