Batman Ninja vs Yakuza League takes place immediately after the events of the first film. Upon returning from feudal Japan to present day, Batman discovers that historical changes have caused an upheaval in the present. Japan has disappeared from the world map and a huge island called "Hinomoto" appears in the sky over Gotham. Batman and his friends head for Hinomoto to seek the cause of the upheaval. There they find a world where the yakuza rule and where there is no honor. Everything comes to a head when Batman and his friends battle Superman and the Justice League, now members of the yakuza, to return the world back to normal.