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In another world, ninja are the ultimate power, and in the Village Hidden in the Leaves live the stealthiest ninja in the land. Twelve years earlier, the fearsome Nine-Tailed Fox terrorized the village and claimed many lives before it was subdued and its spirit sealed within the body of a baby boy. That boy, Naruto Uzumaki, has grown up to become a ninja-in-training who's more interested in pranks than in studying ninjutsu.. but Naruto is determined to become the greatest ninja ever!

A member of the Time Patrol finds out that there is a disturbance in Japan, 1570. While heading to that particular time and location to investigate, she is attacked and ends up stuck underground the Nohara residence at the end of the 20th century Japan. Having limited resources at hand, she is forced to ask for the help of the Nohara family. Together they go back in time and meet with a samurai named Fubuki-maru who believes that they are the legendary three persons and dog whom someone from her family would eventually meet in a crucial moment. The lonely samurai asks for their assistance in defeating the man that possesses strange magical powers, the sinister Unkokusai lord.

It has been two and a half years since Naruto Uzumaki left Konohagakure, the Hidden Leaf Village, for intense training following events which fueled his desire to be stronger. Now Akatsuki, the mysterious organization of elite rogue ninja, is closing in on their grand plan which may threaten the safety of the entire shinobi world. Although Naruto is older and sinister events loom on the horizon, he has changed little in personality—still rambunctious and childish—though he is now far more confident and possesses an even greater determination to protect his friends and home. Come whatever may, Naruto will carry on with the fight for what is important to him, even at the expense of his own body, in the continuation of the saga about the boy who wishes to become Hokage.