The plot takes place after Ultimate Ninja Storm 2 and it begins with the leaders of all villages, the Kages, gathering to discuss the recent terrorist attacks by criminal organization Akatsuki and the involvement of former Konohagakure ninja Sasuke Uchiha on the latest one. Sasuke's group go to attack the Kages as they seek to capture Danzo Shimura, Konohagakure's current Hokage who is responsible for the Uchiha massacre years ago. As Sasuke is weakened in combat against all Kages, Akatsuki leader Madara Uchiha rescues him and request the Kages to hand him over Killer Bee and Naruto Uzumaki as they are the last hosts they need to fulfill their ambitions. The Kages refuse and Madara announces a new shinobi world war as he leaves.
