Team Kakashi returns to the Hidden Leaf Village after completing their mission. As Naruto thinks back to the talk he had with Itachi, he's summoned by Tsunade, where he discovers shocking news regarding Jiraiya.

Shikamaru tries to decipher the dying message Jiraiya left before his death but cannot figure out what it says. Shikamaru asks for Naruto's help, thinking he might know the code. Can the saddened Naruto decipher Jiraiya's dying message?

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

After reading Jiraiya's first book, Naruto becomes more determined than ever to complete his training. Elsewhere, the angered Raikage plans to call all of the kage together for a meeting.

Naruto succeeds in mastering his Sage Mode, taking it farther than even Jiraiya could. Things aren't looking so great for Konoha, however, as Pain prepares to make his move.

The Akatsuki Leader, Pain, begins his invasion of the Hidden Leaf Village. The Leaf ninja assemble to protect Naruto's whereabouts, but when Pain targets Iruka, Kakashi must face off against him.

Tsunade issues an order to call Naruto back to the village, but the elders do not trust her judgment on this issue. While Tsunade tries to convince them and prepares to join the battle herself, Kakashi fights Pain in an effort to figure out his abilities.

When Kakashi falls against Pain, the situation only grows worse for Konoha. Shizune and Inoichi are close to unraveling the mystery of Pain, but when the Animal and Human paths of Pain appear before them, can they escape with the truth about Pain?

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?

Pain confronts Tsunade and questions her about Naruto's whereabouts. Tsunade argues with Pain about his motives, but Pain soon gets the info he needs from another source. Before preparing to depart, Pain unleashes a devastating attack on the village! Meanwhile, Naruto prepares to return to the Leaf Village, but he may be too late.

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.

Naruto successfully begins taking out Pain's bodies one after another, but when his Sage Mode reaches its limit, Pain attempts to take control of the battle. Is the moment of Pain's victory at hand, or does Naruto have a plan?

Pain's God Realm finally enters the battle. As Naruto's toad allies fall one by one, the situation begins to look grim. Can Naruto defeat Pain?

As Pain tells Naruto about why he does what he does, Hinata appears on the scene and confesses her feelings to Naruto. In order to save him, she attacks Pain... Things are about to get messy and Naruto is about to go over the edge!

Naruto's rage pushes him to unleash six of the Kyubi's tails against Pain. In order to combat this menace, Pain is forced to rely upon his most powerful technique to stop Naruto. Will Pain succeed in defeating Naruto, or will the most unexpected of allies appear to calm Naruto down?

The Fourth Hokage appears in Naruto's mind and prevents him from foolishly setting the Kyubi free. Will this confrontation between father and son give Naruto the confidence he needs to stop Pain once and for all?

Naruto confronts Nagato and tells him that he'll give him the answer to the question Pain asked him earlier after he hears about what made Nagato turn to his evil ways. What is Naruto's answer, and what conclusion will Nagato reach?

The Fourth Hokage, Minato Namikaze, left behind his legacy before he passed away. Naruto, Sakura, and Sasuke attempt to find Minato's legacy before the other shinobi teams can get to it.

Naruto, Sakura, Shikamaru, Ino, and Choji continue to search for the Fourth Hokage's Legacy while chasing off some unexpected visitors.

Nagato tells Naruto about how he met Yahiko and Konan and later came to be Jiraiya's disciple.

Nagato reveals the truth about what happened to Yahiko and what made him disregard Jiraiya's ideals. With his story done, he demands to hear Naruto's answers. Will Naruto's answer be enough to convince Nagato to stop his evil plans, or will Naruto be forced to kill Nagato?

With Nagato's story done, Naruto tells him his answer, declaring that he won't abandon the legacy of his master, and he'll keep striving for peace no matter what pain he's put through. Nagato reflects on what Naruto says, thinking back to his final days as one of Jiraiya's students. How will Nagato ultimately respond to Naruto's answer?

Deciding to believe in Naruto, Nagato uses the Gedo Art: Rinne Rebirth jutsu, expending the last of his chakra, and thus giving his life, to revive every person in the village who died in the attack, saying that it's the least he can do. With Nagato dead, Konan leaves Akatsuki, taking Nagato and Pain's God Realm (who is actually the body of Yahiko) with her, parting with Naruto saying that since Nagato believed in him to achieve true peace, she will as well. As Naruto returns to the Leaf, he is astonished to find the entire village awaiting his return, hailing him as a true hero. After all these years, Naruto has finally received the acknowledgment he's always wanted.