The Elemental Nations are once again in danger. But this time they are protected by Yotsukado, the Village of Crossroads. A new ninja village, formed from the combined intentions of all ninja villages, designed to protect and enforce peace throughout all nations.

After the Second Ninja war, the five Great Elemental Nations formed Yotsukado and arranged for ninja from all nations and villages to teach and work there. Their ultimate purpose, to create an international balance system to prevent war, bolster good will between nations, and most of all, to stop any threat like Orochimaru and the Akatsuki from threatening the world again.

A hundred years has passed and Yotsukado is strong. Ninja from all over the lands have come to train and to serve it. But now their skills will finally be put to the test. New threats are dawning.

In Naruto Crossroad you take the role of a rookie Genin transfered from any of the ninja hidden villages to Yotsukado, to begin your training and to help fight against those that would create suffering for their own ends.