After safely escorting the cowardly Takigakure leader Shibuki to his homeland, Naruto Uzumaki, Sasuke Uchiha, and Sakura Haruno are taken aback by the village's sudden invasion of rogue ninjas. As their teacher Kakashi Hatake had departed for Konohagakure beforehand, the team is left to deal with the attacking forces on their own.

While the group prepares for a rescue operation, they learn that Suien, the mastermind behind the assault, is pursuing the Hero Water—an elixir that briefly increases the chakra of those who drink it by tenfold. Knowing that the liquid is in Shibuki's possession, Suien takes the villagers hostage to use them as a bargaining chip.

Despite the odds stacked against them, Naruto fights the enemy heroically, spurring Shibuki on to discover the courage to protect his people.

A month of preparation for the third and final round has passed and remaining competitors are entering the final tournament.

When Konohamaru Sarutobi asks Naruto Uzumaki for help, the latter readily accepts to join his young friend on a special mission—the retrieval of the legendary crimson four-leaf clover, rumored to have the ability to grant any wish. The miraculous plant is seemingly Konohamaru's only hope to prevent the departure of his sweetheart Kaede Yoshino, who must leave Konohagakure on account of her father's job. Despite the unique clover being located in a forbidden area, there is nothing stopping the two from bravely embarking on a perilous adventure to achieve their goal.