In "Batman Ninja," Gotham City's iconic heroes and villains are transported to feudal Japan through a time displacement device created by Gorilla Grodd. The narrative begins with Batman, along with key allies such as Robin, Nightwing, Red Hood, and Catwoman, being thrust into this unfamiliar historical setting. The villains, including the Joker, Two-Face, Penguin, and Deathstroke, also find themselves in this era, where they quickly seize power by allying with warring feudal lords and amassing armies.

The Joker emerges as the central antagonist, consolidating control over the region and establishing himself as a powerful warlord. He transforms the landscape with advanced technology, creating mechanized castles and weaponry that blend futuristic elements with traditional Japanese aesthetics. Batman, initially isolated and without his usual resources, must adapt to the new environment, mastering the ways of the ninja and samurai to combat the villains' growing influence.

As the story progresses, Batman reunites with his allies, who have also adapted to the feudal setting. Together, they strategize to dismantle the villains' strongholds and restore balance. The narrative explores themes of loyalty, honor, and resilience, as Batman and his team face not only the villains but also the challenges of navigating a world vastly different from their own. The climax features a large-scale battle, where Batman confronts the Joker in a dramatic showdown that tests their rivalry in a new context.

The anime incorporates elements of Japanese culture and history, blending them with the established lore of the Batman universe. The characters' designs and abilities are reimagined to fit the feudal setting, with Batman adopting a ninja-inspired suit and the villains taking on roles as warlords and generals. The story concludes with the heroes working to return to their own time, leaving a lasting impact on the world they temporarily inhabited.