While battling Batman at Arkham Asylum, Gorilla Grodd triggers his time-displacement machine, nicknamed the Quake Engine, and hurls him into feudal Japan. There, he is chased by Ashigaru samurai soldiers working for the Joker. During his escape, Batman meets Catwoman, who reveals that everyone else arrived two years earlier due to Batman being in the outermost area affected by the Quake Engine. He learns from her that Gotham City's top criminals have become feudal lords after deceiving the Sengoku daimyo, battling each other until only one state remains. To stop history from being altered, Batman and Catwoman must reach the Quake Engine in Arkham Castle (formerly the Asylum).
Batman discovers that Alfred Pennyworth is also in the past and has built a Batcave outside Edo. When Joker's troops ambush the hideout, Batman storms his way toward Arkham Castle, which transforms into a robot fortress. As Batman confronts the Joker, he is forced to leave and save a mother and child from being crushed by the robot's hand. He transforms his Batcycle into an armored suit to defeat Bane and stop the robot hand, only to learn the mother is a disguised Harley Quinn. As Batman is surrounded by the Joker's minions, he is whisked away by ninja led by Eian of the Bat Clan of Hida.
Batman learns the Bat Clan helped Nightwing, Red Hood, Red Robin and Robin upon their arrival, and the clan has followed a prophecy of a foreign bat ninja restoring order to the land. Robin gives Batman an invitation from Grodd to a nearby hot spring. Grodd explains he intended to send the villains away so he could take Gotham for himself, but Batman's interference sent them to feudal Japan instead. Batman and Grodd agree to work together to return to Gotham. Batman, Grodd, Catwoman, the Bat-Family and the Bat Clan battle the Joker and his forces by the river.
They defeat the Joker and Harley, but Grodd turns on Batman, revealing his alliance with Two-Face before the Joker and Harley escape and blow up their own ship, taking Batman down with it. Having captured a power converter from Harley Quinn, Catwoman attempts to bargain with Grodd in bringing her back to Gotham; however, they need to obtain other power converters from the Penguin, Poison Ivy and Deathstroke to complete the Quake Engine. Two days later, Batman recovers from his wounds and encourages the Bat-Family to learn the ways of the ninja to defeat Grodd.
Red Hood locates Joker and Harley, but Batman discovers they lost their memories from the explosion and are living as farmers. A month later, the villains mobilize their castle robots for battle at the Field of Hell. Batman leads the Bat-Family and the Bat Clan into the battlefield. After defeating the other villains, Grodd controls them with the intent of ruling Japan himself. The Joker and Harley crash his party from above, reclaiming their castle from Grodd. The Bat-Family saves Catwoman and Grodd before the Joker merges all of the castles into the super robot Lord Joker.
An injured Grodd gives the control of his army of monkeys to Batman. Robin enables them to merge into one giant samurai monkey, who in turn fuses with a swarm of bats to form the "Batgod". The Joker reveals to Batman that as farmers, he and Harley planted special flowers that restored their memories after blooming. As the castle falls, Batman and the Joker engage in a sword fight. Using his ninjutsu skills, Batman defeats the Joker. With the Joker and the villains defeated, the Bat Clan begins work to restore feudal Japan and the Bat-Family returns the villains to the present day.
In a mid-credits scene, Catwoman sells weapons and furniture from the castle robots to an antique shop, while Bruce rides a horse-driven Batmobile to a party hosted by the mayor.
