The Batman family has returned to the present to discover that Japan has disappeared, and a giant island - Hinomoto - is now in the sky over Gotham City. At the top sit the Yakuza, a group of superpowered individuals who reign without honor or humanity and look suspiciously like the Justice League. Now, it’s up to Batman and his allies to save Gotham!
In Batman Ninja, Batman is transported to feudal Japan where he must use his skills as a ninja to stop the Joker and his team of supervillains from rewriting history. With the help of his allies and the Bat-family, Batman must navigate ancient Japan and confront deadly foes in order to save the day.