Arc 2Naruto’s First Academy Days

Naruto’s hidden abilities drew the attention of Konoha’s leaders, Kakashi, the Hyuga, and Danzo as he gained greater freedom and began at the Academy. Meanwhile, Obito’s schemes against the Uchiha escalated, and Minato and the Nine-Tails intervened when Obito attacked Izumi, leaving the Nine-Tails’ clone to confront him.

  • Might Guy recognized Naruto’s Flying Thunder God Technique, reported his encounter to Hiruzen, and Hiruzen began considering how to protect Naruto while granting him greater freedom.
  • Kakashi tested Naruto with a lethal attack, but Naruto escaped, and Kakashi later chose to protect him after the Nine-Tails placed a mark on his neck that suppressed his memories.
  • Hiruzen pressed Danzo and the advisers to lift restrictions on Naruto, while the Nine-Tails gathered natural energy and Minato considered the danger posed by the Ōtsutsuki Clan.
  • Obito sent Shisui to Kirigakure to manipulate events around the Three-Tails, while Hiruzen and Shikaku recognized that the Uchiha Clan’s fate had been decided.
  • Naruto started at the Ninja Academy with Hinata and Sasuke, and Neji confronted them before Iruka called them in to register.
  • Itachi agreed to Madara Uchiha’s offer to help with his plan, then warned Naruto to stay away from the Uchiha after rescuing him from the river.
  • Danzo’s Root agents tried to abduct Naruto, but Naruto escaped and reached Izumi, who faced Obito at the Konoha Military Police Force headquarters.
  • Minato took control of Naruto’s body to fight Obito and protect Izumi, then sent a shadow clone empowered by the Nine-Tails to stall Obito while he pursued his plans.
Chapters 26–50 Vol. 1 Read

Ch. 26Guy's invitation

Might Guy discovered Naruto practicing and invited him to train at another location after Naruto showed an unexpectedly polished escape maneuver. Guy also noticed Hinata and her hidden Hyuga guards, leaving them embarrassed when he invited them to join.

  • Two Hyuga guards watched Guy pull Hinata from hiding, and one stopped the other from intervening because he recognized Guy.
  • Hinata fainted after seeing Naruto up close, and Naruto panicked and tried to wake her.
  • Naruto slipped out of Guy's grip with a precise escape maneuver, prompting Guy to wonder who had trained him.
  • Guy helped Naruto settle Hinata aside, and Naruto thanked him and called him a good guy.
  • Guy invited Naruto to train somewhere else, and Naruto agreed but asked about taking Hinata home first.
  • Guy revealed he had spotted Hinata and the two Hyuga guards, then invited them to train too.

Ch. 27Probing, Naruto Makes a Move

Might Guy brought Naruto and the Hyuga guards to his training ground, then tested their readiness with sudden attacks. Naruto repeatedly moved Hinata and the guards out of danger, and the chapter ended with Guy praising Naruto’s Body Flicker Technique and asking him to teach it.

  • Might Guy showed Naruto and the Hyuga guards his training ground, where Hyuga Ichita refused to join in training because they were assigned to protect Hinata.
  • Guy suddenly swung at Hinata, but Naruto whisked her away before the punch could reach her.
  • Naruto warned Hinata and the guards that Guy was dangerous, while Guy stayed silent and watched Naruto closely.
  • Guy attacked again as Hyuga Hengzuo prepared to take Hinata away, but Naruto moved them clear of the blow.
  • Guy praised Naruto’s Body Flicker Technique and asked him to teach it, leaving Naruto, the Nine-Tails, and Minato stunned.

Ch. 28The Flying Thunder God Technique Exposed

Naruto used the Flying Thunder God Technique to protect Hinata, and Might Guy recognized it while pretending it was an extraordinary Body Flicker Technique. Guy warned Naruto to keep the technique secret, while Hyuga Hiashi ordered the clan to spread word of Naruto’s supposed Body Flicker.

  • Naruto protected Hinata from a jōnin, and Guy became fascinated by his apparent Body Flicker Technique and dragged him into the Dense Forest.
  • Guy lost the Anbu who had been following them, then revealed that he recognized Naruto’s technique as the Flying Thunder God Technique.
  • Guy apologized for exposing Naruto’s secret and advised him not to use the technique in front of others.
  • Hyuga Hengzuo and Hyuga Ichita reported Naruto’s feat to Hyuga Hiashi, who ordered them to spread the news that Naruto knew the Body Flicker Technique.

Ch. 29The kidnapping

Might Guy mistook Naruto’s Flying Thunder God Technique for evidence of a dangerous conspiracy and took him away from the Anbu. As Guy arrived at the Hokage Office with urgent intelligence, Hiruzen demanded to know where Naruto was.

  • Might Guy recognized Naruto’s technique as the Flying Thunder God Technique and suspected that a powerful faction had secretly trained the Nine-Tails Jinchuriki.
  • Guy took Naruto and evaded the Anbu, deciding to seek help from the only person in Konoha he trusted.
  • An Anbu reported Naruto’s kidnapping to Hiruzen Sarutobi, who doubted that Guy intended to harm him.
  • Utatane Koharu and Mitokado Homura demanded that the Anbu find Naruto and arrest Guy, while Homura raised suspicions about the Uchiha Clan.
  • Guy charged into the Hokage Office alone and announced that he had urgent intelligence, and Hiruzen asked where Naruto was.

Ch. 30Sarutobi's inner burden

After learning that Naruto had mastered the Flying Thunder God Technique, the Third reflected on Minato and the dangers Naruto faced as the Nine-Tails Jinchuriki. He met Naruto outside his home and, moved by the boy’s kindness, ordered Iruka, Kakashi, and Might Guy to come to his office the next day.

  • Might Guy told the Third that Naruto had returned home safely after using the Flying Thunder God Technique to escape him, and an Anbu reported that Root members were searching for someone.
  • The Third ordered Danzo to come to the Hokage Office and warned him to keep his hands to himself, then heard Guy’s account of meeting Naruto and members of the Hyuga Clan.
  • The Third considered Naruto’s extraordinary talent, Minato’s legacy, and the danger of revealing Naruto’s identity as the Fourth Hokage’s child and the Nine-Tails Jinchuriki.
  • The Third went to Naruto’s home but encountered him outside; Naruto offered him instant noodles and then a ham sausage.
  • After Naruto headed home, the Third asked an Anbu to summon Iruka, Kakashi, and Might Guy to his office the next day.

Ch. 31Kakashi Hatake

The Third spoke with Iruka about Naruto Uzumaki and asked him to look after Naruto when he entered the Ninja Academy. He then walked with Kakashi to Naruto’s home, leaving Kakashi to face an undisclosed task involving the boy.

  • The Third asked Iruka how he viewed Naruto, and Iruka admitted he still struggled to see him as an ordinary child.
  • The Third explained that Naruto was lonely and asked Iruka to look after him when he entered the Ninja Academy before turning seven.
  • After Iruka left, Kakashi reported that Iruka had focused on Naruto and joined the Third for a walk.
  • The Third questioned Kakashi about adjusting to life outside the Anbu and refusing assigned subordinates.
  • The Third led Kakashi to the building where Naruto lived.

Ch. 32The little trio

Kakashi visited Naruto’s home with the Third Hokage, who ordered him to assassinate Naruto. Meanwhile, Naruto trained with Hinata and Sasuke, impressing Hiashi with his abilities and showing Sasuke how to redirect shuriken in midair.

  • Kakashi found Naruto’s home empty of Anbu guards, and the Third Hokage told him to assassinate Naruto.
  • Naruto trained with Hinata at Guy’s training ground, while Hiashi secretly watched and assessed Naruto’s skill and teaching.
  • Sasuke joined Naruto’s training, struggling to match his shurikenjutsu.
  • Naruto demonstrated how to redirect a shuriken into another target, astonishing Hinata and Sasuke.

Ch. 33Assassination

After training with Sasuke and Hinata, Naruto went to Ichiraku alone and sensed overwhelming killing intent on his way home. Kakashi ambushed him, but Naruto dodged the attack, leaving Kakashi surprised by his speed and the power that had awakened inside him.

  • Sasuke left the training ground, vowing to master Naruto’s technique and surpass him next time.
  • Hinata headed home exhausted, and a familiar person warned her to rest and have the clan’s nurse treat her.
  • Naruto ate alone at Ichiraku, paid with the coins he had, and reflected on sensing people’s malice toward him.
  • Naruto felt immense killing intent as he walked, while the Nine-Tails recognized the threat and Minato noticed Naruto’s seal had loosened.
  • Kakashi attacked Naruto with a kunai, but Naruto used his reflexes and the Body Flicker Technique to dodge and appear behind him.

Ch. 34A threat

Naruto outmaneuvered Kakashi’s attack with a clone, but Kakashi revealed his Sharingan and recalled that the Third had assigned him to test Naruto. The Third had explained that Naruto’s exceptional talent could threaten those who could not control him, making his safety increasingly uncertain.

  • Kakashi struck Naruto’s shoulder with Lightning Release, but the injured figure turned out to be a clone.
  • Naruto revealed himself behind Kakashi and explained that he had recognized the standing Naruto as a clone.
  • Kakashi removed his mask and revealed his Three Tomoe Sharingan.
  • Kakashi recalled refusing the Third’s assignment because Naruto was still a child, then agreeing after understanding why the Third trusted him to test Naruto safely.
  • The Third told Kakashi that Naruto had been monitored and faced pressure from Danzo and other Advisors to be controlled or turned into a weapon.
  • The Third explained that Naruto’s growing talent could no longer be hidden and had made him a threat to people who could not control him.

Ch. 35Don't let it happen again

Kakashi tested Naruto with the Lightning Blade, but Naruto escaped using Flying Thunder God and encountered Kakashi’s genjutsu. The Nine-Tails intervened, and Naruto fled to find Sasuke holding his marked kunai.

  • The Third explained to Kakashi that Naruto needed to prove he could survive an attempt to kill him before the village would accept his freedom.
  • Kakashi attacked Naruto with the Lightning Blade, and Naruto dodged by activating Flying Thunder God.
  • Kakashi caught Naruto’s emergence point with his Sharingan and trapped him in genjutsu.
  • The Nine-Tails appeared within the genjutsu, overwhelmed Kakashi, and warned him not to repeat what he had done.
  • Kakashi awoke unharmed and realized Naruto had escaped.
  • Naruto found Sasuke secretly training in the woods, with the kunai bearing the Flying Thunder God Mark in Sasuke’s hand.

Ch. 36The outcome

Naruto told the Third Hokage that a lightning-wielding ninja had attacked him, and the Hokage reassured him while urging him to attend the Ninja Academy. The Third escorted Naruto back toward the attack site, where Naruto prepared for danger but found the street crowded with familiar people.

  • Naruto startled Sasuke at the Uchiha training base, then vanished again before Sasuke could question him.
  • Naruto found the Third Hokage at a Jonin training ground and reported that a ninja with lightning on his hand had attacked him.
  • The Third Hokage reassured Naruto, learned he was unharmed, and encouraged him to study at the Ninja Academy.
  • The Third Hokage escorted Naruto toward the place where he had been attacked while Naruto cautiously watched for danger.
  • Naruto hid behind a tree and leapt out with Shuriken, only to find the busy street full of people, including familiar faces.

Ch. 37The Nine-Tails' seal

After Naruto’s encounter with an intruder, the Third learned from Kakashi that Naruto had displayed extraordinary skill, including using the Flying Thunder God Technique. Kakashi later realized the Nine-Tails had sealed his memories of the fox, and discovered a mark on his neck.

  • Naruto reassured the Third that he could handle himself, while the Third promised to investigate the intruder.
  • The Nine-Tails and Minato Namikaze discussed whether Minato had anticipated the night’s events, and the fox suspected that he had.
  • Kakashi reported Naruto’s exceptional abilities to the Third, who concluded that Naruto should gain greater freedom in the village.
  • Kakashi repeatedly forgot his encounter with the Nine-Tails, then lost strength and accepted Might Guy’s help getting home.
  • The Third summoned Konoha’s advisers to discuss Naruto’s future, while Kakashi discovered a sealing Jutsu mark on his neck and realized the Nine-Tails had affected his memories.

Ch. 38Kakashi's silence

Kakashi examined the Nine-Tails' Mark and realized it could control his actions when he tried to reveal information about the beast. He considered warning the Third Hokage but fell silent as he weighed Naruto's safety against the village's.

  • Kakashi found that the Mark left by the Nine-Tails felt cold and showed no detectable trace of Chakra.
  • Kakashi concluded that the Sealing reacted to his intent to speak about the Nine-Tails by controlling him and making him forget.
  • Kakashi considered bypassing the Sealing and notifying Lord Third, but thought of Naruto and the consequences a report could bring.
  • Kakashi stopped writing as he weighed Naruto's life against the village's safety.

Ch. 39The ban lifted

Kakashi resolved to protect Naruto and the village, and the mark on his neck vanished as he made his choice. In the Hokage Office, Danzo and the advisers accepted Hiruzen’s proposal to lift Naruto’s restrictions and allow him to practice the village’s ninjutsu.

  • Kakashi remembered Itachi’s question about honoring a friend’s wishes and went to Konoha’s Heroes’ Cemetery.
  • At the Memorial Stone, Kakashi recalled his father’s sacrifice and Obito’s belief that comrades mattered more than rules.
  • Kakashi vowed to protect Naruto and the village, and the mark on his neck quietly disappeared.
  • Hiruzen pressed Danzo and the advisers to lift the restrictions on Naruto and let him practice the village’s ninjutsu.
  • Danzo remained silent, and the advisers gave no objection to Hiruzen’s proposal.
  • The Nine-Tails sensed the seal dissipating as Naruto studied and praised him for acting faster than expected.

Ch. 40Akatsuki's debut

The Masked Man brought Shisui Uchiha to Amegakure to meet Pain and recruit him for a mission against the Fourth Mizukage. After Pain tested Shisui and agreed to the plan, the pair left for the Land of Water, with the Masked Man admitting that Akatsuki’s members were using one another.

  • The Masked Man and Shisui Uchiha entered Amegakure, where Konan led them to Pain.
  • The Masked Man introduced Shisui as Akatsuki’s new companion, and Pain attacked him without warning.
  • Shisui evaded Pain’s attack and countered with a shuriken and a Fire Release hand seal, but Pain judged his abilities insufficient on their own.
  • Pain assigned the Masked Man and Shisui to capture the tailed beast from the Fourth Mizukage while he held off Kirigakure’s other forces.
  • The Masked Man told Konan to speed up recruitment, then left Amegakure with Shisui for the Land of Water.
  • The Masked Man stopped during their journey to rest and told Shisui that Akatsuki’s members were merely using one another.

Ch. 41Obito's scheme

Obito Uchiha planned to use Shisui Uchiha’s mission against Karatachi Yagura to frame Konoha and provoke conflict among the hidden villages. Meanwhile, the Nine-Tails inside Naruto felt a surge of delight and revealed natural energy to Minato Namikaze.

  • The Masked Man vanished before Shisui Uchiha could respond, leaving Shisui wary as he realized he had someone else’s eyes.
  • White Zetsu told Obito Uchiha that the Akatsuki had contacted Pain and would reach Kirigakure in time to begin their operation in three days.
  • Obito explained that he had sent Shisui to face Karatachi Yagura, intending to make Shisui a scapegoat if he were captured and use the resulting suspicion to spark a war between the hidden villages.
  • Obito considered Uchiha Itachi as a replacement for Shisui and worried that the Three-Tails’ unexpected strength might indicate that other tailed beasts had also changed.
  • The Nine-Tails inside Naruto felt a rare surge of delight and released some of its energy for Minato Namikaze, who recognized it as natural energy.

Ch. 42A new future

The Great Toad Sage foresaw a new senjutsu tradition arising in Konoha, while Minato Namikaze discovered that the Nine-Tails could gather natural energy inside Naruto's Mental World. Minato and the Nine-Tails continued preparing to change the future and face the threat of the Ōtsutsuki Clan.

  • The Great Toad Sage saw a future in which an entirely new senjutsu tradition was born in Konoha and told the gathered toads that the vision did not concern Jiraiya.
  • Minato Namikaze recognized the energy the Nine-Tails had gathered as natural energy and wondered how it could collect it while sealed inside Naruto's Mental World.
  • Minato questioned whether the Nine-Tails' seal had become merely a formality, and the Nine-Tails insisted it remained trapped.
  • Minato reflected on the threat posed by the Ōtsutsuki Clan and worried that multiple members might attack the shinobi world.
  • Minato and the Nine-Tails continued working toward a new future, with Minato spending time teaching Naruto and the Nine-Tails pursuing its plan.

Ch. 43Darkness of Konoha

Hiruzen Sarutobi and Shikaku Nara confronted the crisis caused by Shisui Uchiha being accused of attacking Kirigakure, while Danzo urged a covert solution to the Uchiha problem. Hiruzen appeared to accept Danzo’s proposal involving Itachi, leaving the Uchiha Clan’s fate seemingly decided.

  • Hiruzen Sarutobi and Shikaku Nara reviewed reports that the Fourth Mizukage had vanished and that Shisui Uchiha was accused of controlling a tailed beast and attacking Kirigakure.
  • Hiruzen and Shikaku discussed how the Uchiha arrests, Shisui’s death, and the village’s inability to reveal the truth had pushed Konoha toward a crisis.
  • Danzo entered the Hokage Office, dismissed Shikaku, and defended the Uchiha’s suppression as necessary despite the lack of evidence.
  • Hiruzen asked Danzo how Shisui had died, then asked what Danzo intended to do; Danzo answered, “Itachi... Uchiha.”
  • After Danzo left, Hiruzen spoke with Shikaku about their sons’ schooling, and both understood that the Uchiha Clan’s fate had been decided.

Ch. 44New shoots

Naruto arrived at the Ninja Academy for his first day, but the sight of children with their families brought back his loneliness until Hinata and Sasuke came to greet him. Their tense encounter with Neji was interrupted by Iruka, who called the children to register, while their families and the Third Hokage watched from afar.

  • Naruto left home excited for his first day at the Ninja Academy, but felt lonely when he saw parents accompanying their children.
  • Hinata and Sasuke surprised Naruto by enrolling early and greeting him at the school gates.
  • Neji arrived to guard Hinata and called Naruto and Sasuke outsiders, prompting a tense standoff.
  • Iruka called Naruto, Hinata, Sasuke, and Neji to stop arguing and come register.
  • Itachi, Hiashi, and the Third Hokage watched the children, while the Nine-Tails let Minato observe through its Chakra perception.

Ch. 45Itachi, what a coincidence

After a mission, Itachi reunited with Izumi and learned more about the Uchiha’s impending rebellion before meeting the masked man at the Naka Shrine and asking for his help. As Itachi returned home, he found Izumi with Naruto, the Nine-Tails Jinchuriki, inside the Uchiha Clan Compound.

  • Itachi completed an Anbu mission, then stopped at a tea stall where Izumi bought him dango and wiped dust from his face.
  • After reporting to the Hokage, Itachi noticed Danzo leave a code and time on the wall, then answered his father’s questions about the village and the clan’s plans for rebellion.
  • Itachi turned down Sasuke’s request for special training and went alone to the Naka Shrine, where he confronted the masked man he identified as Madara Uchiha.
  • Itachi asked the masked man for help with his plan, and the man agreed while inviting him to join Akatsuki.
  • On his way back, Itachi encountered Izumi by the river with Naruto and wondered why the Nine-Tails Jinchuriki was in the Uchiha Clan Compound.

Ch. 46A catalyst for change

Itachi and Izumi talked beside the river while Naruto pretended to sleep, and Itachi warned him to stay away from the Uchiha. Naruto escaped the watchers with a Shadow Clone and Flying Thunder God, while Minato watched the Nine-Tails praise his alertness.

  • Itachi asked Izumi how Naruto had come to the Uchiha compound, and she explained that Naruto often walked Sasuke home after school.
  • Izumi reminisced about her school days with Itachi and hinted at her hopes for a future together, while Itachi stayed silent over the Uchiha Clan's sealed fate.
  • Naruto woke when his clothes caught fire, jumped into the river, and was pulled out by Itachi, who quietly warned him to stay away from the Uchiha.
  • Itachi sensed watchers gathering and offered to escort Naruto out, but Naruto revealed that the boy in the river was a Shadow Clone and vanished.
  • Naruto returned home using Flying Thunder God, and the Nine-Tails praised his vigilance as Minato watched thoughtfully.

Ch. 47Who Are You?

Naruto defeated Sasuke in their Academy match, then left training with him to meet someone. A Chunin claiming to be Naruto’s uncle lured him away, and Minato recognized the man as a member of Root.

  • Naruto beat Sasuke in a close Academy match, while Itachi watched from a nearby rooftop and wondered whether Naruto was using a Shadow Clone.
  • After training, Naruto told Sasuke he had to meet someone, and Danzo ordered his agents to lure Naruto away.
  • A Chunin approached Naruto and Sasuke, claimed to be Iruka’s friend, and invited Naruto to eat ramen.
  • The Chunin grabbed Naruto and, when Naruto questioned him, claimed to be his father’s younger brother.
  • Minato recognized the man as a member of Root after the Nine-Tails shared Naruto’s senses with him.

Ch. 48The Uchiha's Calamity

Terai tried to convince Naruto that he was his uncle, but Naruto escaped and teleported to Uchiha Izumi. There, Naruto and Izumi encountered the masked Obito as he attacked the Konoha Military Police Force, and a water dragon technique struck just as Obito prepared to kill her.

  • Terai spun a story about being Naruto's uncle and tried to keep him from leaving, but Naruto escaped with a Shadow Clone and dispelled it after the Root sensory Ninja exposed it.
  • Naruto used Flying Thunder God to reach Izumi, who was waiting near the Konoha Military Police Force headquarters.
  • Naruto sensed a deadly presence inside the building and warned Izumi that people were disappearing, so she shielded him and prepared for the attacker.
  • Obito emerged from the headquarters, phased through Izumi's shuriken, and bound her with chakra-controlled chains.
  • Obito drew a blade as Izumi called for Itachi, but a water dragon roared from behind him and someone began a powerful Water Release technique.

Ch. 49In the name of the Hokage

Minato Namikaze took control of Naruto’s body and used Sage Mode and Water Release to keep Obito occupied while rescuing Uchiha Izumi. Though the Nine-Tails warned him that intervening could endanger Naruto, Minato chose to fight in the name of the Hokage, and the Nine-Tails agreed to help.

  • When Naruto faltered at the sight of Obito, the Nine-Tails pulled his consciousness into the mental space so Minato Namikaze could act through his body.
  • Minato entered Sage Mode and unleashed a powerful Water Release attack that swept Uchiha Izumi away from Obito.
  • Minato used Flying Thunder God to reach Izumi and keep his identity and abilities hidden while he drew Obito into a pursuit through the water.
  • Minato told the Nine-Tails he intended to keep Obito occupied because he would not abandon the Uchiha Clan while they remained part of Konoha.
  • The Nine-Tails recognized Minato’s resolve and told him to use a Shadow Clone so it could help.

Ch. 50The Nine-Tails Takes Over

Minato created a shadow clone, but the Nine-Tails took control of it and told him to continue his plans. As Naruto wandered inside his mindscape, the Nine-Tails’ clone distracted Obito while disguised as Kakashi, then revealed that it knew his identity.

  • Minato created a shadow clone despite the cost to his Sage Mode and Water Release, and the Nine-Tails took control of it.
  • The Nine-Tails told Minato to leave the fight to the clone and hurry with his plans.
  • Naruto explored the mist-filled mindscape and found the bars of his seal.
  • Obito noticed the Water Release had stopped and tried to identify the person he had been fighting.
  • The Nine-Tails’ clone disguised itself as Kakashi, dodged Obito’s attack, and stalled him.
  • The clone called Obito by his full name and challenged him to continue.
Arc 2 of 25