By using himself as an explosive, Deidara creates an explosion ten kilometers in diameter, something not even Sasuke will be able to escape from. Is this the end of Sasuke? Elsewhere, someone approaches the Akatsuki leader and gives him orders to catch Naruto himself. Who is this true mastermind of the Akatsuki plot lurking in the shadows?

While the members of Team Hebi head towards Itachi's location, Jiraiya infiltrates the Hidden Rain Village in hopes of gathering information on the Akatsuki leader. Jiraiya captures two Rain ninja and interrogates them about Pain, but what he learns shocks even him.

Naruto, Sai, and Yamato arrive to save Hotaru and Utakata from the attacking ninja who they discover are Anbu from the Hidden Mist Village. Yamato attempts to negotiate alone with the head of the Mist Anbu, Tsurugi, and after their discussion, Tsurugi talks to Utakata alone. Tsurugi attempts to convince Utakata to return to the Hidden Mist Village but the latter refuses and remembers the horrible pain he suffered at the hands of his former master.

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.

Without any warning, Zetsu bursts through the floor in the middle of the Five Kage Summit and announces that Sasuke is somewhere in the vicinity. The Summit is immediately put on hold, and the Kages and samurai begin searching for him. Meanwhile, Naruto receives an unexpected visit from Madara, who says that he needs to talk to him. How will Sasuke respond to being discovered, and what are Madara's intentions?

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.

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.

With Killer Bee as his new master, Naruto begins his training to control the power of a Tailed Beast. In order to do so, one must fight the Tailed Beast head on and absorb its chakra, converting it into one’s own power.

Minato is forced to use his Flying Raijin jutsu and leave his wife Kushina behind to save their newborn son, Naruto, from a masked assailant.

The after-effects of Guy's Daytime Tiger are felt throughout the island. Kisame is defeated, and Guy explains his technique. Yamato restrains him so Aoba can gather intel. When he's about to learn Tobi's identity, Kisame forces himself awake by biting off his own tongue. Kisame breaks free of his restraints and creates a water dome around himself. He recalls Itachi's words about learning what kind of person one is when they die. Knowing he's too weak to resist, and to prevent his enemies from gathering intel, Kisame summons sharks and allows himself to be eaten. The others are impressed by Kisame's resolution. When they open the scroll Kisame intended to deliver, it turns out to be a trap, leaving them stuck inside water prisons, while a summoned shark takes the scroll with the intel away.

Kankuro’s commando unit enters enemy territory to set up a stronghold for the Allied Shinobi Forces. They are immediately ambushed by the Akatsuki’s own commando unit comprised of the reanimated Deidara and Sasori.

Kakashi and his unit devise a strategy to take on the Kekkei Genkai shinobi, but it’s foiled by Kabuto, who uses the Reanimation Jutsu to summon the most powerful members of the Seven Ninja Swordsmen of the Mist.

Darui manages to seal away Ginkaku. Fueled by the rage of losing his brother, Kinkaku transforms into a monster that resembles a jinchuriki’s Tailed Beast State.

Naruto and Killer Bee rush to the battlefield when Nine Tails suddenly speaks to Naruto inside his mind. The Nine Tails questions Naruto’s intent to end the hatred in the world and reminds him of how he was unable to save Sasuke.

Kakashi assigns Sai to take over for the Sealing Corps, who are recovering from sealing the reanimated shinobi. But Sai is not sure if he can handle the responsibility. Soon afterwards, the Third Company is attacked by Jinin Akebino.