One year has passed since the events of Rival Schools: United By Fate and that things have gone back to normal in Aoharu City. Batsu Ichimonji, Hinata Wakaba, Kyosuke Kagami, and the rest of the fighters had resumed their normal school lives and that all of them had enjoyed the calm peace that came after their last adventure, but the peace itself doesn't last for long and that the fighters would soon find themselves getting involved in a new struggle. Kurow Kirishima: a cold-hearted and ruthless ninja assassin from a mysterious group known only as the "Reverse Society" has his sight set on the Imawano family and plans to eliminate them and their allies so that he can prepare for the advancement of his own ambition to rule Japan. To this end, he attacks Raizo Imawano: the principal of Justice High and father to Batsu, so that he can easily put him out of commission and not have any interference come from him. Secondly, he sends both his older sister Yurika Kirishima and his loyal subordinate Momo Karuizawa into the ranks of the fighters so that the two of them can cause tension and distrust to occur between the friends. His third plot involves brainwashing Gedo gang leader Daigo Kazama so that he can order him into forcing his gang to attack various schools in order to cause even more tension to occur. Lastly, Kurow himself plans to destroy Batsu's reputation by disguising himself as Batsu's doppelganger (named Vatsu) so that he can attack the fighters and make them believe that Batsu is behind it. Batsu and his friends must fight back against the evil plot of Kurow and attempt to not let their friendship get destroyed by the conspiracy of a deadly ninja assassin.