"RAIL WARS!" is set in an alternate version of Japan where the national railway system remains privatized, focusing on the daily operations and challenges faced by railway employees. The story centers on Naoto Takayama, a high school student and aspiring railway worker who joins the Japanese National Railways (JNR) training program. Naoto dreams of a peaceful career in the railways but finds himself thrust into unexpected situations when he is assigned to the Public Security Division, a special unit tasked with handling railway-related crimes and emergencies.

Naoto is paired with a group of trainees, including Aoi Sakurai, a disciplined and serious girl with a strong sense of duty; Shou Iwaizumi, a laid-back but skilled individual with a knack for mechanics; and Haruka Kōmi, a cheerful and energetic girl who often provides comic relief. Together, they navigate the complexities of railway operations, from managing passenger safety to thwarting sabotage attempts by anti-JNR groups. The series blends slice-of-life elements with action and drama, showcasing the intricacies of railway systems while exploring the personal growth and relationships of the main characters.

The narrative often highlights the contrast between Naoto's idealistic view of the railways and the harsh realities of the job, such as dealing with bureaucratic challenges, terrorist threats, and the moral dilemmas of enforcing rules. The Public Security Division frequently encounters situations that test their teamwork and resolve, from preventing train accidents to uncovering conspiracies that threaten the railway network. Throughout the series, the characters' dedication to their roles and their passion for the railways are emphasized, offering a unique perspective on a profession rarely explored in anime. The story balances lighthearted moments with intense scenarios, creating a dynamic portrayal of life within the railway industry.