After the invasion of the Hidden Leaf Village by ninja from the Hidden Sound and Sand villages, the game begins with the epic battle between Orochimaru and Third Hokage of the Leaf Village.
As the battle rages between the elite ninja, Orochimaru reveals he has mastered a horrible new ninja technique. The Hokage loses the fight, but as he is about to die, he manages to make Orochimaru's arms useless, so that he cannot use any more Jutsu. His sacrifice forces Orochimaru and his lieutenants to beat a hasty retreat.
With the Sand and Sound ninjas defeated, the rebuilding of the Leaf Village begins. Jiraiya, a ninja master, is selected to leave the village and find the next Hokage - a ninja named Tsunade. He asks Naruto, now a well-respected ninja, to help him in his quest - and pick up some new ninja skills along the way.
Naruto's new abilities trigger the envy of his best friend and ninja team-mate, Sasuke, who has his own reasons for wanting power.
Sasuke is out for vengeance against his brother Itachi, who massacred their entire family when Sasuke was a child. Sasuke is shocked to realize he's still not strong enough to go after his brother. He was once the best ninja of his age, but now Naruto might be surpassing him.
Orochimaru takes advantage of the situation and asks Sasuke to leave his friends and his village in order to join his evil clan and become more powerful. Orochimaru's intentions are not clear, but the promise of power might be too much for Sasuke to turn down.
Can Naruto and his friends save Sasuke?