Naruto returns and discovers that the village has been devastated by Pain's Shinra Tensei attack. Naruto requests that everyone stays back as he prepares to take on all six paths of Pain at once.

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.

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.

As he is resting, Naruto starts dreaming his past experiences with Sasuke that made the two friends closer. When he tries to follow Kakashi, who is in pursuit of Sakura, he is stopped by Yamato, saying that he has orders from Kakashi to return Naruto to Konoha. Naruto devises a plan to sneak out and leaving a shadow clone to fool Yamato. He goes into Sage Mode to locate Kakashi. He then starts remembering the experiences that brought Sasuke pain in his life. Naruto decides what he can do for Sasuke if they come face to face.

Tsunade sends out Naruto under the guise of a top-secret mission to keep him hidden away from the Akatsuki. Unfortunately, Naruto, Yamato, Gai, and Aoba are stuck at the pier due to a report of a monster attacking ships.

Shikamaru begins to feel the pressure of shouldering the lives of his friends in the upcoming Fourth Shinobi World War. To help ease his mind, Shikaku sends his son along with Tenten on a mission to Mokuzu Island to replenish supplies.

While talking with his students, Shino talks about how he and his team got together and became more close as friends and teammates. The story switches to Shino's flashback during the first part of Naruto. They are on a mission assigned by Kurenai in which a Jonin assassin from a neighboring village. Shino gets defeated because of weak taijutsu and descends into depression. He even reveals he was going to abandon the team that helped him because he didn't think he was useful to them. But after his friends get in trouble with the rouge Shino comes back and defeats the rouge.