A port of the Japanese game, Naruto RPG 3, the game's story takes place during the anime's "filler" period between Sasuke's leaving the Hidden Leaf village to the time jump that restarts the series several years later. Instead of following the various mini-plots that the show possesses, the game's story is original and all new. A group of rogue ninja have started a plot to bring about an ancient evil, and it is up to Naruto and the rest of the cast to stop this force once and for all.
While the game takes place outside of the show's normal timeline, players will still get to relive many of the major battles that already happened in the form of flashbacks. It seems that Naruto's adventure will take him to many places that we have already seen in the show, and when he gets to one of these locations, the player will have to reenact the fight. I'm sure these battles include Naruto versus Sasuke, or Squad Seven taking on Zabuza and Haku, or even the Chunin Exams since some of the characters the developers hinted at would only be available in these particular flashbacks.