Naruto Uzumaki is a young boy who has the Nine-Tailed Demon Fox sealed within him. Twelve years before the start of the series, the Nine-Tailed Demon Fox attacked the ninja village Konohagakure, slaughtering many people. In response, the leader of Konohagakure – the Fourth Hokage – sacrificed his life to seal the demon inside Naruto when he was a newborn. Konohagakure, however, regarded Naruto as if he were the demon fox itself and mistreated him throughout most of his childhood. A decree made by the Third Hokage forbade anyone mention the attack of the demon fox to anyone. Years later, Naruto was tricked by the renegade ninja Mizuki into stealing a forbidden scroll, but was stopped by his teacher, Iruka Umino. Once he realized he was tricked, Naruto uses the Shadow Clone Technique from the scroll to defeat Mizuki. That encounter made Naruto realize he was the container of the demon fox.
The main story follows Naruto and his friends' personal growth. Naruto befriends two comrades, Sasuke Uchiha and Sakura Haruno, who are assigned with him to form a three-person team under an experienced sensei named Kakashi Hatake. Naruto also befriends other characters that he meets throughout the series. They learn new abilities, get to know each other and other villagers better, and experience a coming-of-age journey as Naruto dreams of becoming the Hokage of Konohagakure. At first, emphasis is placed on Naruto, Sasuke, and Sakura, who are the members of Team 7. Later, Orochimaru, a criminal at the top of Konohagakure's most wanted list, attacks Konoha killing the Third Hokage as an act of revenge. This causes one of the three legendary ninja, Jiraiya to search for his partner Tsunade, to become the Fifth Hokage. During that search, it is revealed that Orochimaru also desires to acquire Sasuke Uchiha due to his powerful genetic heritage. Believing Orochimaru will be able to give him the strength needed to kill his brother Itachi, who destroyed all his clan, Sasuke goes to him. Naruto does not give up on Sasuke, leaving Konoha for two-and-a-half years of training to prepare himself for the next time he meets Sasuke.
After the training period, a mysterious organization called Akatsuki attempts to capture the nine powerful tailed beasts including the Nine-Tailed Demon Fox sealed inside of Naruto. Several ninjas from Konohagakure, including Team 7, fight against the Akatsuki members search for their teammate Sasuke. Sasuke, however, betrays Orochimaru and faces Itachi to take revenge. Although Itachi dies, Sasuke is told by the Akatsuki member Madara Uchiha that Itachi was ordered by Konohagakure's leadership to destroy his clan. Saddened with the revelation, Sasuke joins forces with Akatsuki to destroy Konohagakure. Meanwhile, as several Akatsuki members are defeated by the Konohagakure ninja, the leader, Pain, prepares to invade the village to kidnap Naruto.