Manmaru is a modest penguin recruited as a ninja trainee by an old man named Jiya. He joins a long-standing conflict between ninja clans inhabiting Jiya's mountains. His fellow trainees initially express disappointment, viewing him as overly polite and somewhat flaky despite expectations for a formidable recruit.

He trains at the Nenga ninja school alongside anthropomorphic animals like foxes and raccoons, under a bear ninja master. His training involves navigating rivalries with other factions: the Koga, represented by monkeys, and the Iga, represented by dogs. He also faces challenges from the Dobe, a group of Nenga dropouts attempting to lure trainees away from their studies.

Physically, Manmaru has large, distinctive eyes and adheres to the common anthropomorphic penguin design seen in anime of his era. His journey requires navigating clan conflicts and resisting external temptations that test his dedication to ninja principles. The series structure implies progression through training challenges and interpersonal dynamics within this setting.

Beyond the core series, Manmaru appears in a Sega Saturn platform game. In this adaptation, he struggles to master the Nenga Clan's divine art. His master sends him to a Ninja Mansion to refine these abilities, framing the game's objective around this skill development journey.