"Gekijō-ban Anime Nintama Rantaro Ninjutsu Gakuen Zenin Shutsudō! no Dan" is a feature-length anime film based on the long-running "Nintama Rantaro" series, which is set in a ninja academy where young students train to become skilled ninjas. The story revolves around Rantaro, Shinbei, and Kirimaru, three first-year students at the Ninjutsu Academy, who are known for their comedic misadventures and struggles with their studies. The film expands on the series' episodic format, presenting a larger-scale narrative that involves the entire academy.

The plot begins when the Ninjutsu Academy receives a mysterious letter warning of an impending crisis. The academy's headmaster, Doi-sensei, decides to mobilize all students and faculty to investigate the threat. The students, including Rantaro and his friends, are divided into teams and sent on a mission to uncover the source of the danger. Along the way, they encounter various challenges, including rival ninja groups, hidden traps, and puzzles that test their skills and teamwork.

As the story progresses, it is revealed that the threat is linked to a legendary ninja artifact with immense power. The artifact has been stolen by a rogue ninja faction seeking to use it for their own gain. The students must work together to retrieve the artifact and prevent it from falling into the wrong hands. The narrative balances humor, action, and moments of camaraderie, staying true to the tone of the original series.

Key characters include Rantaro, a cheerful but clumsy student who often relies on his quick thinking; Shinbei, a studious and serious boy who struggles with self-doubt; and Kirimaru, a gluttonous yet talented ninja with a carefree attitude. The film also features recurring characters from the series, such as the strict but caring Doi-sensei and the eccentric teachers who guide the students on their journey.

The climax of the film involves a large-scale battle between the students and the rogue ninja faction, showcasing the students' growth and the bonds they have formed. The resolution emphasizes the importance of teamwork, perseverance, and the values of the ninja way. The film concludes with a return to the academy, where the students reflect on their experiences and prepare for future challenges.