Ultimate Ninja Storm 3 begins with the attack of the Nine-tailed Demon Fox of the Konohagakure ninja village while its former leader, Third Hokage Hiruzen Sarutobi, tries to stop it. The current leader of Konohagakure, Fourth Hokage Minato Namikaze, faces the masterminds behind the attack: Madara Uchiha and the fox. The story then moves to some time after Ultimate Ninja Storm 2‘s; the five leaders of the ninja village face Sasuke Uchiha, who intends to kill acting hokage Danzo Shimura. Madara saves Sasuke and declares a world war against the ninja forces. In the next chapter, Sasuke’s former comrades from Konohagakure try to kill Sasuke until Naruto Uzumaki convinces him to have a death match. Naruto trains to obtain the power of the fox with the help of Killer Bee and the spirit of his mother, Kushina Uzumaki. The fourth ninja world war begins, with the ninjas facing the Madara’s army of Zetsu and Kabuto Yakushi’s reanimated warriors. When Naruto and Killer Bee go to war, Kabuto revives the original Madara Uchiha and reveals that the “other Madara” is an imposter. While the five Kages make Madara retreat, Naruto defeats the fake Madara forces.
After the story mode’s ending, a side story reveals that Sasuke is joining the war. He changes sides when he allies with the reanimated body of his brother, Itachi, to defeat Kabuto and send his forces to the afterlife.