"Shin Kotaro Makaritoru! Judo Hen" centers on Kotaro Makaritoru, a young and ambitious judoka striving to master the art of judo and achieve greatness in the sport. The narrative begins with Kotaro entering a prestigious judo dojo, where he faces intense training and formidable opponents. His journey is marked by a series of challenges, both physical and mental, as he hones his skills and develops his unique judo techniques. The story emphasizes the importance of discipline, perseverance, and respect for the martial art, reflecting the core values of judo.

Kotaro's growth is driven by his encounters with various rivals and mentors, each contributing to his development as a judoka. The series delves into the intricacies of judo techniques, showcasing detailed depictions of matches and training sessions. Key characters include Kotaro's sensei, who provides guidance and wisdom, and his fellow trainees, who serve as both allies and competitors. The dynamic between these characters adds depth to the narrative, highlighting themes of camaraderie and rivalry.

As Kotaro progresses, he participates in numerous tournaments, each presenting new obstacles and opportunities for growth. The stakes rise as he faces increasingly skilled opponents, culminating in high-stakes matches that test his abilities and resolve. The series balances intense action with moments of introspection, exploring Kotaro's motivations and the broader philosophy of judo. Through his journey, Kotaro not only aims to become a champion but also seeks to embody the spirit of judo, striving for personal and technical excellence.