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.

Unleashing a devastating surprise attack, flying ninjas from the Land of Sky are seeking revenge against their old enemy Konohagakure. Despite his eagerness to join the fight, Naruto Uzumaki is held up by Shinnou, a mysterious doctor who requires his assistance to save an injured person. While delivering the wounded man to the hospital, Naruto has an unexpected encounter with Amaru—a stormy youngster from a neighboring village desperately looking for Shinnou's help. Meanwhile, as the invaders withdraw to restore their forces, Tsunade seizes the opportunity to dispatch a small team including Sai, Shikamaru Nara, and Kakashi Hatake to strike down their base. Simultaneously, she commissions Naruto, Sakura Haruno, and Hinata Hyuuga to accompany Shinnou and Amaru on their journey. During this time, however, Orochimaru has his own schemes: he orders Sasuke Uchiha to bring him the doctor who specializes in the reincarnation technique. As the escort group accidentally uncovers the sinister truth behind the attacks, tumultuous plans are set in motion. But even when confronted with an unforeseen reunion, Naruto does not waver in his endeavor to end the warfare and its disastrous effects.

A group of ninja is planning to revive a powerful demon, and once its spirit is reunited with its body, the world will be destroyed. The only way to prevent this from happening is for Shion, a shrine maiden, to seal it away for good. Naruto Uzumaki is tasked to guard her, but one thing stops Shion from accepting his help: she also has the ability to predict death—and she has foreseen his demise approaching soon. In order to escape his fate, Naruto must stay away from Shion; however, undeterred, he chooses to challenge the prophecy in order to protect Shion and the world.

Led by Yamato, Naruto Uzumaki, Sakura Haruno, and Sai are assigned to capture Mukade, a rogue ninja who is pursuing the ancient chakra Ryuumyaku located underneath the Rouran ruins. While the Ryuumyaku has been sealed by the Fourth Hokage, the group fails to prevent Mukade from releasing its power. Consequently, a strong energy burst engulfs both Naruto and Yamato before they can escape. As he awakens in a magnificent yet hostile kingdom, Naruto meets its young queen Saara and three Konohagakure ninjas on a top-secret mission. They reveal to him that he has time-traveled to Rouran 20 years into the past! To make matters worse, Mukade has already infiltrated the royal court, becoming the naive queen's most trusted minister under the alias Anrokuzan. Joining forces with the three ninjas, Naruto must protect Saara's life without fail to stop the villain's plans and return to the present.