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.

As the Fourth Great Ninja War quickly approaches, Sunagakure hosts a special Chunin exam to strengthen the troops of the Allied Shinobi Forces. Among the participants are Konohamaru Sarutobi, an ambitious rookie, and Naruto Uzumaki, who has become a renowned ninja. Despite the significant disparity in skill, Konohamaru is excited at the prospect of proving himself in a competition against Naruto—the one person he both admires and sees as his rival.

After being sent to investigate the alarming disappearance of four bloodline limit-wielding ninjas from different countries, Kakashi Hatake, Naruto Uzumaki, Sakura Haruno, and Sai successfully discover their whereabouts and inform the Hokage. Unexpectedly, Tsunade's further arrangements fall apart when Hiruko—the mastermind behind the incident and also a former Konohagakure ninja obsessed with power—appears to announce that he has absorbed the missing ninjas' unique abilities. On the verge of becoming invincible, he seeks one more bloodline limit before starting an all-out war to take over the world. As Konohagakure's past connections with Hiruko raise suspicions among the nations about its involvement in the affair, Tsunade receives an ultimatum to solve the crisis. Left with no other choice, she decides to follow Kakashi's lead after he presents a daring yet salutary scheme—a proposal that could send him to certain death. However, Naruto opposes such a plan! Despite the Hokage's decision, he is determined to save his teacher's life, even if it means fighting friend and foe alike.

Led by Kakashi Hatake, Naruto Uzumaki, Sakura Haruno, and Rock Lee are tasked to escort the extravagant Prince Michiru Tsuki and his spoiled son Hikaru to the prosperous Land of Moon when the two return from a long trip around the world. As if guarding two whimsical high-ranked individuals was not challenging enough, the prince's reckless decision to acquire an entire circus during their journey—mainly to entertain Hikaru's wish of owning the saber-toothed tiger featured in the show—further propels the mission into disarray. Just as things are finally settling down, the arrival of Michiru's convoy at the Land of Moon is met with an unforeseen crisis—the greedy Chief Minister Shabadaba has taken over the country with the assistance of mysterious, powerful ninjas. While Kakashi's team relentlessly fights the enemy by any means necessary, the two princes are forced to confront a new outlook on life through adversity.