The story of Naruto Shippuden: Ultimate Ninja Storm 3 is about the various ninja villages being at war. What I liked about this game is that they took what the first two games did and kept what people liked all the while making various little improvements to the formula.
This is an awesome series of games and you can actually get the whole original trilogy in one collection these days. Naruto Shippuden: Ultimate Ninja Storm 3 is following on from where its predecessor left off.