Naruto, two jonin and an elder known as "the Eternal Genin" set off to a mission to patrol the border of the Land of Fire following Orochimaru's attack. After some days with no incidents, a group of enemy ninjas cross the borders. The Eternal Genin proves to be a brave ninja and remembering the lessons he learned with the 2nd and 3rd hokages, sees the similarities between Naruto and his father.

Naruto thinks back to the time when he encountered the soul of a man named Kisuke. Kisuke didn't recall anything about who he was, but a visit to the Leaf Village's hospital revealed something startling. Meanwhile, higher-ups of the Fire Country met to decide on a new security system for the Leaf Village put together by a ninja named Sabiru. Who exactly were Kisuke and Sabiru, and what connection did the two have?

Iruka struggles to deal with his hate for the Nine-Tailed Fox inside Naruto as he tries to connect with Naruto after seeing him shunned by his peers.

After discovering a kunai knife with a secret message on it, Naruto winds up being pursued by three kunoichi from the Hidden Waterfall Village. Iruka mangaes to find him, but when the situation grows worse, Kakashi appears to save them both.

After having discovered that the village was under the control of rebels from the Hidden Rain Village, led by Hanzo, Naruto and Jiraiya decided to take action to help save the women and children taken hostage and free the village from the Rain's tyrannical control.

Konohamaru's team asks Neji to talk about Naruto's heroism. Instead, Neji tells them about an incident during the Chunin exams three years prior. While Orochimaru attacked Konoha, two rogue ninja take advantage of the commotion and kidnap Hinata. Neji, Tenten, Kiba, and Akamaru rush out to save her. They're in trouble until Hiashi shows up and saves them, telling Neji that he's the beloved memory of Hiashi's younger brother. Neji realizes Naruto's speech about destiny was right; he isn't just a slave to the clan name. Konohamaru's team complains that Naruto wasn't in the story at all, and Neji cryptically answers that Naruto was the most important part.

Naruto thinks back to the time when Team 7 was on a mission to capture a group of thieves who stole a golden statue. When making a move on the thieves, Naruto and Sasuke had managed to take back the statue but were separated from Sakura, who was captured. On top of that, the thieves' leader had used a special thread-like technique to bind one of Naruto's hands to one of Sasuke's. Literally stuck to each other, would Naruto and Sasuke be able to work together to save Sakura and keep the golden statue safe at the same time?

Shikamaru remembers the time when Teams 7 and 10 joined together to flush out a band of bandits who were terrorizing a nearby village and had kidnapped the headman's granddaughter. With no assistance available from Kakashi or Asuma, Shikamaru was forced to lead the team of genin to the bandits' fort and come up with a plan to rescue the headman's granddaughter.

In the aftermath of the destruction of the Leaf Village, Iruka thinks back to the time when the Third Hokage first gave him the task of being Naruto's homeroom teacher at the Academy, since no one else would take him in.

After hearing the news about Akatsuki's attack on the Hidden Leaf Village, Gaara worries about Naruto's well-being. He remembers a time in the past where Team 7 was assigned to help him out with a problem, and how nobody, especially Naruto, was eager to trust him. Yet, when his life was put in danger by people he had wronged, Naruto was the first to come to his rescue.

Sakura reflects upon a time when she was infected with a strange disease by Naruto. In order to find a cure, an order was issued for Naruto to be quarantined at all costs before he could infect anybody else.

While she and Neji prepare to visit an old man who makes ninja weapons, Tenten remembers the first time she visited him alongside Naruto and Neji. Utilizing a strange new weapon she had never seen before, Tenten fought against two ninja who had stolen two of the man's powerful weapons.

A female spy, Hanare, from the Hidden Lock Village (Land of Key) is caught by ANBU pretending to be a musician. She is interrogated. However, the interrogation proves unsuccessful. Slowly, her past is revealed and so is her relationship with Kakashi. Team 7 spy on the two as they go around town, under the impression that the two are dating. After The Lock Village keeps a Leaf Village ninja hostage, they exchange Hanare for the ninja. It is then revealed that Hanare has a special ability, causing a large chase to occur. In the end, Kakashi lets Hanare free. The musician seen at the beginning entertaining Konoha ninja reminds Kakashi of Hanare which prompts the flashback.

During the two-and-a-half-year time period in which Naruto was training under Jiraiya, the latter decided that it was time for Naruto to learn how to repel genjutsu. During this training session, the two traveled to a village which Jiraiya had previously been associated with, but they discovered that something dark was amidst.

In the past, Naruto and Sakura joined Sasuke on a mission to collect the paw print of Nekomata, a large and powerful two-tailed ninja cat that ruled over all of the ninja cats.

Sasuke has a flashback while traveling to Konoha with his team, Taka. He once saved a girl named Naho not knowing that she's a relative of the Feudal Lord. Meanwhile, Naruto and Sakura are sent on a mission to accompany Naho and act as her bodyguards while Kakashi and Sasuke are sent to discover the reason why internationally wanted bandits have entered their border. Kakashi and Sasuke later find out that the bandits intend to abduct Naho. Naruto and Sakura are defeated by the bandits and are taken hostage. Sasuke finds them first and proceeds to defeat the leader and mercilessly punches him because of his jealousy for Naruto's growing power. A cut to the present reveals Naruto contemplating on his promise to have Sasuke return to the village.

Kakashi has a flashback back when he was assigned to be the sensei of Team 7. In a bid to know his students, Naruto, Sasuke & Sakura, better, Kakashi spies on them and to see how they would all get along as a group. Angered by Sakura's talk about calling Naruto a brat and that he has no family to tell him right or wrong, Sasuke tells Sakura she is annoying. Realizing Sakura's sadness, Naruto goes to battle Sasuke, but gets defeated. It then goes back to the present and Kakashi claims that it is up to him to stop Sasuke.

As the ninja of the Hidden Leaf Village work on repairing their village in the aftermath of Pain's invasion, Naruto and Sakura come across a familiar face among the carpenters: Inari and Tazuna have arrived to help out. Inari recalls what happened after Gato's death and how Naruto and Sasuke came to his rescue.

In a flashback of Naruto and Sakura's, Team 7 is on a mission to take an ostrich called Mr. Ostrich to his home. They arrive at a village where they see a swordsman named Tsukado who has a vendetta to carry on a man named Katazu who killed his distant relative Shikazo. Tsukado fails to defeat him so Naruto decides to teach him unusual revenge lessons. Katazu has then took his brother's identity and attracted Shikazo's pursuers while Kageki and his family went into hiding. Tsukado decides not to kill him and ends their years of fighting though Kanabun wants them to keep fighting. The swordsmen, Team 7 and Mr. Ostrich chase the Kanabun Gang out of town.

An ostrich tells a story of when Naruto, Rock Lee, and Shino, all led by Kotetsu, entered the Leaf Village's animal district in an effort to find and subdue him. However, he and the other animals proved that they weren't willing to go down without a fight.

Back before Rock Lee had his surgery, Naruto, after donning the suit given to him by Guy, set out on a mission with Sakura and Ino to obtain a special flower which was a necessary ingredient for Lee's medicine. When Naruto picked one of the flowers, however, he had to face a strange technique that had taken on the form of Gaara.