The story mode is split into Part I and Part II, each part features different characters or different version of the the same characters. the RPG elements that was featured in the Story Mode of Naruto Shippūden: Ultimate Ninja Storm 2 were removed, the game focuses on the battles and offers faster gameplay from previous games, the use of the substitution Jutsu is now limited by a new status meter. The game also offers new side-stories for different supporting characters.

The game offers a new mode called "Beast Mode" ( known as Awakening Mode ) where the playable characters will have the ability to turn into a strong beast whenever they are about to lose. The game also features a way to unlock special content and fighting abilities by using real collectable cards .

- Beast Mode -