Sakura is caught by Sasori’s tactic and surrounded by a poison cloud.

In the Rain Country, Jiraiya decides to take care of three young orphans for a while. Yahiko, a spunky young boy, wants Jiraiya to train him, Konan, and Nagato to be shinobi, but it's not until he sees a strange phenomenon in Nagato that he decides to do so. What is the secret behind Nagato's Rinnengan eyes? What will become of these three children?

Itachi reveals to Sasuke that Madara is the second culprit behind the Uchiha massacre, as well as the history of the Mangekyo Sharingan and the first two Uchiha to obtain it: Madara and his brother. One question still remains: Why did Itachi really spare Sasuke's life?

The code Jiraiya left behind is finally deciphered, but what exactly does it mean? Meanwhile, Naruto continues his training.

Ebisu protects Konohamaru from Pain and refuses to divulge any information about Naruto. Ebisu is willing to give up his life in order to protect both Naruto and Konohamaru. Konohamaru isn't about to let his teacher throw his life away, but what can he possibly do against Pain?

As Naruto and Sasuke clash, their Rasengan and Chidori explode, sending them both flying. When Zetsu and Madara appear to aid Sasuke, they decide to retreat to the Akastuki headquarters. Before they leave, however, Naruto has one last thing to say to Sasuke; something that will have an impact on both of their lives.

As they continue their voyage towards the Land of Lightning, Naruto, Aoba, Guy and Yamato sail through a thick fog. To pass the time, Yamato tells Aoba and Naruto some ghost stories (much to Naruto's dislike).

Konohamaru is eager to fight alongside his senior ninja in the coming war, but his young age prevents him from being assigned to the battlefield.

Kiba trains hard to catch up to Naruto, who is now hailed as the hero of the Leaf Village, but with little success. Feeling desperate, Kiba asks Kakashi if he could train him.

The Nine Tails, having been released from Madara's control, continues to wreck havoc in the city. The Third Hokage summons the Monkey King Enma and drives the Nine Tails away from the city. Minato then returns to the city and with the help of the toad Gamabunta is able to restrain the Nine Tails long enough for him to teleport it along with his family to the outskirts of the village. Kushina binds the Nine Tails and as Minato prepares to do the Reaper Death Seal to seal away half of the Nine Tails Chakra and seal the rest inside Naruto using the Eight Trigrams Seal. He also seals a bit of Kushina's chakra to help Naruto tame the Nine Tails. All of this is witnessed by the Third Hokage and a few other ninja.

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.

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.

While the Saezuri is revealed, learning that Disonasu employed Kabuto Yakushi to wipe out the residents of Tonika Village, Dokku tried to attack Disonasu, but stopped by a reincarnated puppet and restrained by a resurrected Takigakure shinobi.