Tsunade is caught in the Infinite Tsukuyomi. In it, she falls asleep and dreams of being given Jiraiya's latest work and recalls when he was still writing it. She begins reading it.
In the novel, Naruto lives in Konohagakure and is a member of Team Kakashi. His parents did not die during the Nine-Tailed Demon Fox's Attack, in which the half of the Nine-Tails was sealed into him while the other half is sealed within his mother. The villagers dislike Naruto, but show him some respect as he is the Fourth Hokage's son. People often accuse Naruto of favouritism due to this, which angers him. The Uchiha Clan Downfall also never happened as Minato and Hiruzen were able to succeed in negotations; as such Itachi never defected the village, nor did Sasuke. Naruto begins to learn how to use the Nine-Tails' chakra, and Nagato did not die from attacking Konoha and both he and Konan join Naruto later on. The Nine-Tails' also had no interest in getting out of Naruto, but was helping to guide him to learn how to control its power, even telling Naruto it is too soon for him to wield its power or during his battle with the Six Paths of Pain that he is too angry to control its power properly.
Team Kakashi, Team Kurenai, Team Asuma, and Team Guy are given a mission to find experienced shinobi who have gone missing, under the assumption that as they're recent Academy graduates, they won't be targeted by whoever is behind the abductions. During the mission, the jōnin leaders are kidnapped. Akatsuki is revealed to be behind the abductions, and Team Asuma briefly battles Konan, Yahiko, and Nagato. The Konoha genin discover an abandoned village. In the village, Teams Kakashi and Guy briefly see their kidnapped allies, Naruto and Neji give chase, and end up meeting a masked man who possesses the Byakugan. Team Jiraiya goes down a sinkhole to rescue two children, who came back to the village, and end up fighting a couple of creatures in an underground lair.
Team Asuma aids Team Jiraiya in rescuing the children from the underground creatures. Chōji is attacked by one of them, and is saved by Nagato. The two teams return the children to their mother. Team Jiraiya thanks Team Asuma for coming to their aid, and surmises they also share some of Jiraiya's values. Team Jiraiya asks them to join, but Team Asuma refuses, wanting to find Asuma. Shikamaru deduces Team Jiraiya does not want them dead, and is following orders from someone else. They prepare to fight again, but Team Jiraiya leaves just before they're joined by Team Kurenai. Shikamaru does not tell them about Team Jiraiya, and decides they need to both report to Konohagakure and regroup with Teams Kakashi and Guy. Lee and Sasuke discuss about returning to the village or keep looking from their vanished team-mates and sensei. The masked man takes Naruto and Neji through a gate, where they are shown images from the Hyūga Affair. The three discuss the events witnessed, and the masked man asks Neji to join him and force change in Konohagakure. Elsewhere, Jiraiya finds one of Orochimaru's compounds.
Being asked, Neji questions the masked man's motives. He says that by changing how a village such as Konohagakure operates, the other hidden villages will follow, changing the world for the better. The masked man requests Neji to see what he means. Neji agrees to hear him out, and when Naruto tries to interfere, the masked man paralyses him. Neji promises to return to Naruto once he has seen what the masked man wants, and the two depart. Jiraiya ventures into Orochimaru's hideout, and comes across a bandaged individual. Team Jiraiya reports to the masked man about the incident with the children, including how the Konoha genin eventually helped them, despite the directives of their mission. The masked man ponders about it, and instructs them to resume surveillance. Neji asks if the Konoha genin are his team-mates, which the masked man confirms, and asks Neji if he wants to see if they can change the future of shinobi. Naruto tries in vain to access the Nine-Tails' chakra. Sasuke and Sakura discuss the mission's situation. Lee and Tenten search for Neji and Guy, which Kiba smells from a distance. Hinata spots Neji and the masked man observing Sasuke and Sakura, as well as Sasori. Sasuke detects Sasori's presence and attacks, and Sasori begins to fight the two. Teams Asuma and Kurenai head out towards Sasuke and Sakura. Lee and Tenten are attacked with explosive tags, directing them towards the same location. Sasori lands a hit on Sasuke, poisoning him. The Nine-Tails tries to convince Naruto to open the seal so it can use its chakra to aid Naruto. Jiraiya suddenly appears to Naruto.
During the battle against Hiruko, the masked man prevents Neji from coming to Sasuke and Sakura's aid, assuring him he won't let them be killed, insisting Neji watch the battle to witness their true selves. The masked men reminds Sasori of the mission, and Sasori begins attacking Sakura, who manages to dodge his attacks and land one of her own, causing Sasori to retreat. She proceeds to treat Sasuke, removing the poison in his system. The masked man tells Neji there is more to come. Jiraiya clears Naruto's blocked tenketsu. Naruto asks him why he's there, and he explains he's searching for someone, and when he heard of what was happening, he had Minato transport him there using the sealing formula incorporated in Naruto's seal. Jiraiya tells Naruto to try summoning a toad, but it fails. Jiraiya recalls Naruto's training, and Naruto recalls training with Minato. Jiraiya offers to weaken the Eight Trigrams Sealing Style a bit. Lee and Tenten stop running, Tenten noticing they're no longer under attack. They're met by teams Asuma and Kurenai. The two update them on what has happened with Neji and Naruto. Kiba smells Sasuke and Sakura nearby, and Hinata spots Sasori near them. While Sakura heals him, Sasuke thinks back to his childhood. Sasuke looked forward spending time with Itachi, but Itachi was summoned by Minato, so he suggests Sasuke spend time with their father, who compares him unfavourably to Itachi when he tries the Fire Release: Great Fireball Technique for the first time. Sasuke detects Sasori, who approaches them again and brings out his hundred puppets. The other genin reach the two, and the masked man retreats with Neji. Sasuke intends on getting reinforcements from Konoha. Team Jiraiya watches from afar, discussing the situation. Jiraiya weakens Naruto's seal, causing him to develop four tails.
He then battles the four-tailed Naruto, who destroys his Chakra-Suppressing Seal. He manages to immobilise Naruto. Jiraiya thinks back to Gamamaru's prophecy. Sasuke thinks back to being unfavourably compared to Itachi by their father and begins fighting Sasori's puppets. The other genin join the fight to protect Sasuke. Team Jiraiya observes the fight. The masked man and Neji debate on the genin's motivation to fight. Sasori reveals spare puppets. Naruto thinks back to his Rasengan training with Minato, and manages to suppress the Nine-Tails' chakra. Jiraiya retreats, and sends Naruto to help his team-mates. Naruto manages to use the Rasengan, and uses it and several clonesto dispatch Sasori's puppets, causing him to retreat. The genin congratulate Naruto, and decide to look for their kidnapped team leaders. Neji asks the masked man if his test has yielded the results he expected, and surprises him by calling him father.
Neji asks about the kidnapped shinobi, and the masked man tells him Team Jiraiya will take him there. The masked man leaves Neji to reunite with his comrades. The Konoha genin join as one team, and discuss how to find the kidnapped shinobi. They're joined by Neji. The masked man appears to Team Jiraiya, Hidan, Kakuzu, and Sasori, telling them the test is over. Hidan, Kakuzu, and Sasori leave, while ordering Team Jiraiya to take the evacuated villagers back to their homes, as well as one other thing. Neji finishes explaining the nature of the experiment they participated in. Konan creates paper butterflies to lead the genin to the captured shinobi, and leaves with her team. The genin find the captured shinobi and release them. Kurenai asks them about the recent events, and the masked man arrives, offering to explain it himself. He removes his mask and bandages, revealing himself as a reincarnated Hizashi Hyūga. Neji explains the Hyūga Affair, and Hizashi explains how he was reincarnated by a bandaged man, and orchestrated the incident to ascertain if his death had effects on how Konohagakure handles its affairs. Hizashi and Neji discuss Neji's motivations, and how there were changed after fighting Naruto. Neji's words allow Hizashi to let go of his attachments, and his soul is released. Yahiko sets off to the village to return Komichi his teddy bear Kenta. An explosion suddenly wipes out the village, and Nagato spots Kenta damaged, and grows furious, believing Yahiko to have been killed.
After retrieving their team leaders, the genin teams return to the village and Minato decides not to punish them for disobeying orders because their actions resulted in the mission's success. After being scolded by his father and having a talk with his brother about the relation between the Uchiha and the village, Sasuke starts training with Kakashi to learn the Chidori. At the same time, Naruto undergoes training with Jiraiya and Minato to enhance the Rasengan. Increasingly jealous of Naruto becoming stronger, Sasuke starts treating his team-mates with disdain and, after being stopped by Minato while having a fight with Naruto, asks his father to have him transferred from Team 7 to the Konoha Military Police Force. Determined to become stronger to gain Sasuke's acknowledgement, Naruto leaves to train with Jiraiya while Sakura undergoes training with Tsunade. Meanwhile, Orochimaru meets with Danzō, who promises to find someone as a suitable vessel for the former. Three years pass as the members of Team 7 continue their training and return to Konoha. After hearing of Sasuke's increased prowess and performance rivaling the likes of Itachi and Shisui, Fugaku gives his son a rank of lieutenant in the Konoha Police Force.
In the following weeks, Sasuke and his unit drastically reduce crime and disorder throughout the village, however they do so through exceedingly strict and aggressive means, causing an equal drop in morale throughout the villagers as the people grow nervous and distrusting of them. While Minato and Hiruzen are unsure of how to approach this as officially Sasuke's unit has done nothing wrong, Naruto soon returns to the village after completing his training with Jiraiya. Upon his arrival, he stops Sasuke's unit from harassing a old woman for opening up her shop too early. Eager to finally settle things with Naruto, Sasuke engages Naruto in battle. Their scuffle is quickly ended by the arrival of Danzō, who notes that Naruto has grown strong and that Sasuke is lacking what he could become.
As word begins spreading throughout the village about how Sasuke's unit backed off from Naruto's intrusion of their duties, Sasuke's men began fearing that they lost the people's respect and decided to arrest Naruto. They quickly intruded into Naruto's home and threatened Kushina. This unauthorised act resulted in themselves being arrested. Fugaku, greatly displeased as Sasuke's lack of maturity and morals, removed Sasuke from the Police Force completely. Further embittered by from getting no respect, Sasuke approached Danzō about his earlier words. The elder explained that he didn't trust Naruto wielding the power of the Nine-Tails and wanted a good countermeasure against him. To which, he told Sasuke about Orochimaru, a Sannin like Naruto's teacher Jiraiya, and where to find him. As Danzō contacted Orochimaru about his new potential host body in Sasuke, Sasuke made his choice to leave the village, knocking out the guards. He is then confronted by Kakashi, who questions his actions. Sasuke explains that while he is grateful of Kakashi, he is not satisfied with his progress and is going to "the other Sannin" to gain power before knocking Kakashi out with genjutsu. After waking up in the hospital, Kakashi informs Tsunade, along with Minato and Hiruzen, of Sasuke leaving to meet with Orochimaru. Wanting to avoid putting the Uchiha clan in a worse position, Minato orders an emergency lockdown and makes preparations to find Sasuke. Unknown to them, Sakura overhears everything and goes to tell Shikamaru, who asks the rest of Konoha 11 to meet in their old classroom.
Knowing Orochimaru only wants Sasuke as his next vessel and Sasuke is unaware of this, they agree to bring him back no matter what. Naruto and Shikamaru, the only ones required for the task, use a Kiba and Akamaru's secret escape tunnel to sneak out of the village. Before leaving, Naruto promises to Sakura that he will bring Sasuke back. Kushina alerts Minato that Naruto snuck out of the house and his friends are acting suspicious, but Minato calms her down and assures her that Naruto is likely training elsewhere. Danzo sends four members of the Anbu out to stop Naruto and Shikamaru from reaching Sasuke, even giving them command to kill the two and anyone else who interferes. As Naruto and Shikamaru are attacked, Team Guy arrive to be a back-up. Seeing the Anbu is trying to kill them, including Naruto, Shikamaru realises these Anbu don't serve Minato and Neji says he heard rumours of a secret faction of the Anbu called Root being led by someone else. The group decides to split up and allow Neji, Tenten, and Rock Lee deal with some of the Anbu while giving Naruto and Shikamaru time to catch up with Sasuke. Meanwhile, some members of the Akatsuki regroup after Deidara kills a group of Sand shinobi. It is revealed that Deidara was responsible for the explosion that killed Yahiko and Sasori lied to Nagato and Konan that Minato and Konoha were the culprits. Enraged, Nagato vowed revenge against the village and joined the Akatsuki.
By the time they reach the tower Sasuke is at, Shikamaru orders Naruto get inside while he deals with another Anbu. Sasuke meets Orochimaru and demands power, which Orochimaru grants him by inflicting him with the Cursed Seal of Heaven. Naruto is stopped by another Anbu who possesses the Wood Release and a frustrated Naruto starts to fall under the Nine-Tails' influence, forming four tails in the process. The Anbu tries to hold his transformation back but the desire to stop Sasuke allows Naruto to overcome the Nine-Tails and defeats the Anbu. When he finds Sasuke, who is already adapting to his new powers, Naruto is angry at Orochimaru for what he's done to Sasuke, who challenges Naruto to a fight to test his new powers. Naruto enters Sage Mode and begins to fight him while vowing to bring Sasuke back with force if necessary. Sasuke summons Kirinand is able to impale Naruto, while confessing that he always hated Naruto for getting stronger. Naruto, shocked by Sasuke's actions, admits that he always felt they were alike because they grew up in their fathers' shadows and he always like being friends with Sasuke. Using the Nine-Tails' chakra to heal himself, Naruto throws Sasuke his headband and Sasuke puts it on, acknowledges Naruto as an equal, and mocks Naruto he won't be able to scratch it. Naruto subconsciously starts to use the Nine-Tails' chakra while Sasuke enters his cursed seal second stage, and the two prepare to finish the battle with Chidori and Rasengan. Much to their shock, Itachi suddenly appears in the middle and is struck by Sasuke's Chidori, asking Naruto to get along with his brother and pokes Sasuke's forehead before disappearing as he "dies". Their attacks collides and Sasuke emerges as the winner as Naruto lays unconscious on the ground. Orochimaru picks up Sasuke's headband and comments how entertained he is, and Sasuke leaves with Orochimaru while remembering his brother and awakening the Mangekyō Sharingan.
Naruto is later found by his friends and learns that Sasuke got away. He, however, reaffirms his promise to Sakura and learns from Shikamaru that the Anbu retreated once Sasuke escaped, which makes him suspect that their mission was to make sure Sasuke got to Orochimaru. Back in Konoha, Tsunade informs Minato that Kakashi will be supervising during the night. Shizune alerts them that someone has entered in the village and they are confronted by Pain, whom Tsunade realises looks like Yahiko. When asked what he wanted, Pain declares his intent to make the village suffer for the pain it put him through by destroying the village that killed Yahiko, but Minato, Tsunade, and Shizune don't know what he's talking about. He uses True: Chibaku Tensei to encase the entire village in a satellite. By morning, Naruto and the others return to find the village has disappeared. They meet with Sakura, who explains she was on a mission and doesn't know what happened. Neji uses his Byakugan and says the villagers are alive in the satellite. Naruto wants to rescue them but Sakura insists that he needs to recover from his injuries and heals him. They are confronted by the Six Paths of Pain and fight Naruto, who enters in Sage Mode. When normal jutsu doesn't work, Minato comes up with a plan for him, Kushina, Hiruzen, and Tsunade to use the Four Red Yang Formation to prevent the walls from crushing them and buy them time. Naruto is able to take down all but one of the Pains until he is pinned down by Deva Path when the limit for Sage Mode runs out. Hinata enters the battlefield and declares she is not afraid to die protecting Naruto. However, she is easily defeated and impaled by Pain. Enraged by this, Naruto transforms into the six tailed stage and goes on a rampage against Pain, who tries to trap him in another Chibaku Tensei.
Sensing that the Nine-Tails' chakra is unstable, Kushina and the others believe something is wrong with Naruto. Ino contacts Shikamaru and he informs them of Naruto's situation. Kushina decides to meet with her son in his subconscious and transfer her half of the Nine-Tails into him, even though Minato warns her that it will kill her. Naruto vents his anger for Pain for what he's done and asks the Nine-Tails for more chakra, but the beast points out Naruto is not able to properly control his powers. Naruto is surprised that Kushina is able to meet him and she explains how, when the Nine-Tails attacked the village, Minato sealed half of it into her and the other half into her because they had faith Naruto could control his powers. After explaining her decision to transfer her half of the Nine-Tails power into him to help him gain control of both Nine-Tails, Naruto initially protests because she will die but he decides to have faith in his mother.
Before doing so, the two Nine-Tails halves note that only giving half of Yin-Kurama's chakra to Naruto will be more than enough to aid Naruto without sacrificing Kushina's life. Agreeing to these terms, the mother and son bump fists, transferring the extra chakra into Naruto. Naruto then proceeds to enter an incomplete Tailed Beast Mode to break free of the Chikabku Tensei before enters in Nine-Tails Chakra Mode and charges at Pain. Rather than killing him, Naruto uses one of Pain's Black Receiver to locate Nagato's hideout. When they meet, Nagato justifies his actions as part of seeking to avenge Yahiko from Konoha, but Naruto insists Konoha always believed it was Nagato and his comrades who destroyed the village Yahiko died in. Nagato says he no longer cares who was responsible because it won't bring back Yahiko. Naruto says he understands the pain of losing a comrade because Sasuke is in danger of becoming Orochimaru's vessel but he truly believes they can reach an understanding because they are friends. Naruto also asks Nagato to let him join Team Jiraiya because not only he is a student of Jiraiya but he wants to cooperate with all the shinobi. Nagato is shocked of how similar Naruto's words are to those Yahiko once spoke and releases the True Chibaku Tensei. The village is restored and everyone is unarmed, and Nagato and Konan disappear.
Minato thanks Fugaku for his service in protecting the village but says there are no leads on Itachi's and Sasuke's whereabouts. Fugaku feels guilty for neglecting Sasuke in favour of Itachi, but Minato assures him they are still likely getting along. At Orochimaru's hideout, Sasuke attacks Orochimaru and kills him before collapsing and passing out from poison. When he wakes up, he recognises Sasori, who asks Sasuke why did he kill his brother and Sasuke looks at him sadly. Sasori goes on to say those who deserved to die didn't and Sasuke decides it should have been Naruto who died rather than Itachi. As Sasori offers to have the Akatsuki help him, Sasuke announces his goal to destroy Konoha in order to get revenge on the village for controlling the Uchiha clan.
At Konoha, Tsunade informs Konoha 11 that Sasuke killed Orochimaru and is allying with the Akatsuki, as well as that the organisation has been attacking the other hidden villages and kidnapping several high ranking shinobi. With the intel Jiraiya has gathered, Naruto and his friends set out to the Akatsuki's hideout. Sasori brings Hidan, Deidara, Kakuzu, Zetsu, and Sasuke to show them his puppet army which he says he amassed to rule the world. Sasuke seems doubtful of his decision and when Sasori confronts him, Sasuke explains he doesn't want to destroy Konoha but he simply wants to change the ninja system. He also says he never agreed to join the Akatsuki. Sasori and the others learns Konoha 11 have reached the area and go out to confront them. Sasuke is shocked when he sees Itachi appear in front of him. Itachi says he actually survived from his injuries and he came back to make Sasuke realise the wrong path he was following before disappearing.
Sasori, Deidara, Hidan, Kakuzu, and Zetsu face off against Konoha 11. Deidara places numerous explosives in the group, but Sasuke arrives and uses lightning to deactivate them, surprising Naruto and Sakura. Sasuke explains he still doesn't consider them comrades but he will help them. Sasori reveals his true face and uses his puppet collection to fight them, but Minato, who had come back from a Kage Summit, arrives on the scene with Gaara and numerous other shinobi of the other villages to help. They seal away the puppets and Sasori faces off against Naruto, Sasuke, and Sakura. Revealing that he turned the Raikage, Mizukage, and Tsuchikage into puppets, Sasori says he lost so much military strength for it and he had sought out Sasuke to make up for the loss, leading Sakura to realise Sasuke is innocent on the allegation of joining the Akatsuki. All three use the Summoning Technique, but Aoda is defeated. Jiraiya arrives with Nagato and Konan to assist, and say Naruto will be the new member of Team Jiraiya. Sasuke tries to fight alone, but Itachi arrives and saves Sasuke from the Mizukage's Lava Release, berating him for not working with his comrades. The brothers both use their respective Susanoo and defeat the Kage puppets. Naruto tells Sasori that all he needs is his comrades before finishing him off with a combination of Rasenshuriken and Sasuke's Kagutsuchi. With the battle over, Naruto asks Sasuke to return to the village so they can start over and be friends. Sasuke agrees to return, but says he will change the world in his own way.
Back at the tower, Naruto reaffirms his vow to bring Sasuke back and they begin their battle. Sasuke explains they were destined to fight since they first met at their Academy entrance ceremony, but Naruto rebuffs this. Sasuke goes on that he had started wanting to surpass Naruto when the latter jumped in a river to save a puppy while Sasuke was too afraid of drowning, and this made Sasuke feel he was weak and prompted him to use any means to get stronger than Naruto. However, Sasuke also admits that while he hated the village for ostracising the Uchiha clan, he came to respect the Hokage for saving the clan from revolting and he started to acknowledge Naruto, which disgusts him now. Naruto uses shadow clones but Sasuke uses Susanoo and destroys the clones, except for one that is gathering chakra for Naruto to enter in Sage Mode. Naruto trades blows with Sasuke with his Rasenshuriken but their attacks destroy the tower and send them flying to the ground. Realising Sasuke is serious about killing him, Naruto asks the Nine-Tails to lend him some power and learns the beast's name is Kurama. In Nine-Tails Chakra Mode, Naruto uses Tailed Beast Ball against Sasuke's attacks but this drains them of chakra. They then punch each other in the face and are knocked down. Sasuke admits he was always jealous of Naruto and Naruto takes Sasuke's hand, saying he will always be there as a friend. After this, Sasuke admits defeat, returns to the village, and all of Konoha 11, with Minato, Nagato, Konan, and Gaara pose for a photograph.
Tsunade is half-sleep and says it was a good ending. When she wakes up, she is surprised to see Jiraiya but it turns out to be Dan, who is wearing the Hokage hat. He tells her they are going to be late for the Five Kage Summit, and as they are walking down the hall, she sees Orochimaru and Jiraiya with Nawaki. She becomes enraged at Jiraiya for trying to give her brother a dirty book. In reality, Tsunade is trapped in the Infinite Tsukuyomi.