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.

During their discussion of a sensitive investigation A, the Fourth Raikage, and his subordinates are ambushed by a cloaked intruder. As the Kumogakure leader repels the assault, he is shocked to discover that the culprit is Naruto Uzumaki! However, the assassination attempt is not the only crime attributed to the young ninja, who vigorously denies the accusations. To avoid a diplomatic conflict, Tsunade forcibly sends him to Kusagakure's Houzuki Castle—a maximum-security penitentiary dedicated to ninja criminals—until the situation is resolved. Despite his powers being immediately suppressed by Mui, the prison's warden who possesses the ability to seal chakra, Naruto recklessly engages in futile escape attempts. But with the help of two fellow inmates, he realizes that there is more to this legendary detention facility than meets the eye. Uncovering a terrible secret, the trio embarks on a dangerous operation that may be Naruto's only chance to break free and prove his innocence.

In a tumultuous effort, the Sunagakure ninjas attempt to repel an unforeseen invasion of mysterious armored warriors on the Land of Wind. Shortly afterwards, the same armored troops led by Temujin—a skilled knight of impressive power—ambush Naruto Uzumaki, Sakura Haruno, and Shikamaru Nara, who are on a mission to recover a lost ferret. Naruto and Temujin engage in a fierce fight that ends with both of them falling off a cliff. Taken aback by their friend's sudden misfortune, Sakura and Shikamaru witness yet another alarming development: a massive moving structure appears out of nowhere, ravaging any trees and rocks in its path. While Sakura sets off to find Naruto, Shikamaru infiltrates the imposing fortress in hopes of learning more about the critical situation. Entangled in a relentless conflict, the Konohagakure ninjas join forces with their Sunagakure counterparts to defeat the common enemy. However, amidst the turmoil, a clash between two different visions of an ideal world emerges.