The Confining the Jinchūriki Arc spans from chapters 489 to the current manga. All the Five Great Shinobi Countries have formed a ninja alliance with the Land of Iron and prepare for the Fourth Great Shinobi World War and the final battle against Akatsuki. While Naruto trains to control the Nine-Tailed Demon Fox's power. It also describes the Nine-Tails' Attack on Konoha.
Summary
Preparing for the War
Tsunade is eating a lot to rebuild her chakra reserves. She is then greeted by Kakashi, who is relieved that she is alright, as it would have meant him becoming Hokage, and he feels he isn't cut out for it. Tsunade orders a meeting to make preparations for the coming war. Elsewhere, Ibiki interrogates Karin on information about Sasuke and Kabuto.
The Great Toad Sage has seen a vision of Naruto, and would like to see him before he decides whether or not he should receive the key to his seal. Naruto is enjoying some ramen, when Sakura informs him of Tsunade's recovery; this leads to his next meal being declared "on the house". As he is about to eat, he is reverse summoned to Mount Myōboku, to receive the premonition; the Sage sees "octopus tentacles" and "a young man with powerful eyes". Naruto listens to what he has to say, and accepts what ever lies ahead.
Anko and her team have located a number of bodies, evidently victims of Kabuto. The fact that he just left them there and made no attempt to hide them leads the team to suspect a trap. Meanwhile, Kabuto has located Madara, briefly shows of his new abilities, resurrecting Itachi, Deidara, Kakuzu, Sasori and Nagato, and offers an alliance with Madara. Kabuto asks for Sasuke to test out his ninjutsu. Madara asks if he refuses and Kabuto summons another casket with an unseen body that shocks Madara. Madara then accepts the offer under the condition that Kabuto cannot be anywhere near Sasuke until the end of the war. Nearby, Anko and her team discover Kabuto has joined with Madara and she wonders what his motive is and reports the news to Konoha.
Back at Myōbokuzan, Naruto signs the contract to the key, knowing he is ready to control the Nine-Tails and Gerotora stores himself inside Naruto. Naruto asks the Great Toad Sage about where to find the octopus but only tells him he sees an island paradise. Fukasaku sends Naruto back to Ichiraku where two Konoha ninja ask for his autograph. At Kumogakure, A calls a short meeting with the other Kage.
Confinement
A convenes another meeting for final preparations before the war
Three days later, the Kage discuss the enemy's power and confining the Jinchūriki. Tsunade is outraged by confining Naruto and Bee saying they would help greatly in the war though Gaara and Ōnoki calm her down telling her it was decided. A says Naruto and Bee will be confined on a island in Kumogakure that him and Bee train at.
As Naruto, Yamato and other Kohoha and Kumo ninja arrive at the island, a giant squid (who Naruto thinks is the octopus the Great Toad Sage spoke of) appears and grabs Naruto until he is saved by Bee in his full eight-tailed transformation. One Kumo ninja, Motoi greets them and guides them through the island. While guiding them through the island, they are confronted by King, a large gorilla that Bee has tamed. Motoi tells Naruto not only can he control the beasts on the island, but he can also control the Eight-Tailed Giant Ox, learning Bee is also a jinchūriki.
Later, Naruto asks Bee if he can help him control the Nine-Tails and Bee refuses. Naruto tries a rap but messes it up by unintentionally insulting Bee and tries to fix it with the Harem Technique though Bee slams the door on Naruto. Naruto goes to Motoi to ask him how Bee trained to control the Eight-Tails and shows him to the "Falls of Truth", the first step of how Bee learned to control his tailed beast.
Nine-Tails Control Training
Dark Naruto appears before Naruto
At the Falls of Truth, Motoi tells Naruto to sit in front of the waterfall and close his eyes when an evil version of Naruto appears from the waterfall. Dark Naruto begins to insult the real Naruto, stating that he's an impostor and insults him over the choices he's made, which angers Naruto. They fight but Naruto realizes that they are both evenly matched so the battle ends in a tie.
When he wakes up and tells Motoi about his encounter with the Dark Naruto, Motoi tells him that he has to defeat Dark Naruto to control the Nine-Tails. Meanwhile, Killer Bee is fighting with some bears in a competition. Eight-Tails try to persuade him into helping Naruto but fails. Also, Motoi reveals something from his past: he once tried to kill Bee himself but failed. When Naruto and Yamato asks why, he begins to reveal about the Eight-Tails' bloody history. Long ago, Eight-Tails had several hosts, and each failed to control it. After each host lost control, the Eight-Tails had rampaged through Kumogakure several times. Each time it rampaged, the Third Raikage and other elite shinobi came to stop it, and sealed it inside a sealing jar. Each time the beast was resealed many shinobi would lose their lives, one of these was Motoi's father. Almost immediately after Killer Bee was chosen to be the new host, Motoi thought it was pointless and the beast would go on a rampage again. Because of his father's death, his hate of the Eight-Tails grew out of control and Motoi attempted to kill Killer Bee. He was quickly dispatched and Killer Bee stuck out his hand, for his customary fist bump. After which Motoi ran away not speaking to Killer Bee again.
After Motoi's story, Naruto goes off to think if all the villagers and his friends trust him. Suddenly Naruto hears Motoi being attacked by the giant squid which he mistakes for Bee again. Naruto and Yamato begin to assault the squid until Bee arrives again this time punching a hole through the squid. After being saved by Bee, Motoi tells Bee he tried to kill him years ago and Bee easily forgives him which brings tears to Motoi and they bump fists which causes Naruto to smile.
Later on, Bee thanks Naruto for helping Motoi and they become friends. Bee then becomes willing to teach Naruto how to control the Nine-Tails. They return to the Falls of Truth where Dark Naruto surfaces again noticing a change in Naruto. Naruto states he has faith in himself and hugs Dark Naruto which causes him to disappear into Naruto. With the darkness eliminated inside of him, Bee takes Naruto to a a sacred place behind the waterfall where he will fight the Nine-Tails. They approach an entry box where Naruto activates a switch and opens a door to a large empty room.
Naruto fights the released Nine-Tails in his subconscious
Naruto approaches the Nine-Tails within his subconscious and removes the seal, thus releasing the beast. Naruto tries to use his chakra with the help of Bee to pull the Nine-Tails' chakra but it slices the Eight-Tails' tentacles and pulled away. It then realizes Naruto is trying to take control of it. Naruto and the Nine-Tails begin their battle where the Nine-Tails fires a huge concentrated blast of chakra at Naruto. Bee uses the last of the Eight-Tails' power to block the attack and Naruto in Sage Mode uses the Sage Art: Super Great Ball Rasengan on the Nine-Tails, though it blows it away with a roar. Naruto flips the Nine-Tails over and slams Wind Release: Rasenshuriken on it, giving him a chance to drain its chakra.
While taking its chakra, some of the Nine-Tails' hatred is pulled in, causing Dark Naruto to reemerge. Bee notices the Nine-Tails' hatred is larger than he expected and Yamato tries to tame Naruto from the outside. The Nine-Tails tells to Naruto to disappear when suddenly Kushina appears and tells him he belongs "here", with her hand on her chest.
Naruto meets his mother for the first time and hugs Kushina out of joy
Kushina has Naruto guess who she is with Naruto claiming her to be the Nine-Tails' true form which causes Kushina to clobber him on the head. Kushina apologizes to Naruto and he realizes she is his mother and hugs her, causing Dark Naruto to disappear again. Outside Naruto, the transformation stops which surprises Bee and Yamato. Before Naruto begins asking his mother about her, Kushina chains up the Nine-Tails where it notices it's Kushina's chakra. Naruto asks Kushina how she and Minato fell in love which embarrasses her though she tells him any way.
When she first met Minato, she thought he looked like a wimp and wanted to be the first female Hokage. Other kids laughed at her because of this and also her face and hair features with the kids calling her tomato. She eventually got back at the kids, giving her the nickname, the "Red Hot-Blooded Habanero". Kushina had a special chakra and was once kidnapped by Kumogakure because of this. Kushina left a trail of her hair that only Minato noticed. Naruto complements Kushina's hair which she states is the second time someone complemented her hair, the first time being Minato. Being the son of "Konoha's Yellow Flash" and the "Red Hot-Blooded Habanero", Naruto gives himself the nickname, "Konoha's Orange Hokage".
Hearing his mother saying she loves him, Naruto releases himself from the Nine-Tails' hatred and resumes his battle with Kushina holding the Nine-Tails with her chakra. Naruto attacks the Nine-Tails Spiralling Super Large Group Spheres and Sage Art: Super Great Ball Spiralling Large Group Spheres and slams it with one more Rasenshuriken where successfully pulls out the Nine-Tails' chakra. Once its chakra was pulled away by Naruto, the Nine-Tails gathers chakra for one last attack, but is stopped by Naruto, who's seal, the Nine-Tails noted, reminded it of the Sage of the Six Paths. As Naruto resealed the Nine-Tails into a new seal, the Nine-Tails warned Naruto that it would not forget this.
Truth of the Nine-Tails Incident
After the Nine-Tails defeat, Kushina says to Naruto she can see Minato again. Before going, she decides to tell Naruto the truth of the Nine-Tails incident 16 years ago and she reveals she was the Nine-Tails' former jinchūriki.
Kushina explains that after Hashirama Senju defeated Madara, his wife, Mito Uzumaki, volunteered to become the first Nine-Tails jinchūriki. As she was about to die of old age, Kushina was brought to Konoha to be the new Nine-Tails' jinchūriki due to her special chakra. Mito comforted her and told her that love could save her from loneliness and the responsibility of housing the Nine-Tails, which in Kushina's case was her love for Minato. She tells Naruto that Madara came after the Nine-Tails as soon as Naruto was born because he somehow knew that when a female jinchūriki gives birth, the seal weakens.
Kushina was giving birth to Naruto outside the village with Biwako Sarutobi serving as the midwife and Minato holding the seal so the Nine-Tails wouldn't break free. As Kushina had given birth to Naruto, Madara (explained by Minato as the member of the Akatsuki with a mask) appears and swipes Naruto and threatens to kill him if Minato didn't back away from Kushina.
When Minato hesitates Madara throws the newborn Naruto in the air threatening to kill him with a kunai causing Minato to come to Naruto's aid, catching him before Madara could kill him. Just as soon as Minato had caught Naruto he realizes there were exploding tags on Naruto's back. Minato manages to escape the explosion using his Flying Thunder God Technique. He then transports himself and Naruto to his house, leaving Naruto there for the time being so he would be safe.
Meanwhile, Madara has captured Kushina and extracted the Nine-Tails from her. With the power of the Sharingan, Madara is able to control the Nine-Tails and uses it to kill Kushina, who is still alive after having the Nine-Tails ripped out of her. Before the fox could kill her, Minato quickly transports to Kushina, and saves her from the attack. Kushina then warns Minato of Madara and the Nine-Tails heading for Konoha. Minato transports Kushina to the house and sets her down next to Naruto. Thankful their child is alright, she hugs Naruto and cries in relief. Seeing this, Minato is angered and prepares to go after Madara and the Nine-Tailed Fox, with Kushina wishing him luck.
Elsewhere in the village, Itachi who is trying to calm an infant Sasuke and Kakashi and Guy get a strange feeling in the air. Hiruzen Sarutobi feels the slight presence of the Nine-Tails' chakra. Madara, after sneaking into the village, summons the Nine-Tails directly into the village, causing destruction and death instantly. Hiruzen prepares for battle, even as he is notified of the Nine-Tailed Demon Fox's attack, and orders nearby shinobi to protect the village. Minato teleports back to the village, and when the Nine-Tails spots him and attacks him, uses a space-time barrier to counter the Nine-Tails' attack. Madara confronts Minato himself, and tries to send Minato to another dimension but Minato teleports himself to a nearby forest, but Madara follows. There, Minato deduces that the masked attacker is Madara Uchiha, though Madara gives no definate answers when asked. They both begin to fight until Minato gains the upper hand and uses a Rasengan to knock Madara into the ground. Then while Madara is standing up, Minato uses a seal that broke Madara's control over the Nine-Tails. Then Nine-Tails was driven outside the gates of Kohona. Meanwhile Kurenai Yūhi's father is forbidding Kurenai and the rest of the ninja of rank away from the battle, while in the battlefield itself a young Iruka Umino is protected by his mother while his father orders him to get away.
Returning to Konoha, Minato is horrified at the destruction and summons Gamabunta on top of the Nine-Tails while it was creating another blast of chakra. Minato then teleports him and the beast away from Konoha, letting the Nine-Tails' attack detonate away from anyone. Minato meets up with Kushina, who is nearly out of chakra but uses her chakra chains to hold down the Nine-Tails. She tells Minato her plan to reseal the Nine-Tails into herself and die with it, giving them all time until the Nine-Tails returns. As Minato cries at this thought, she tells Minato that her only regret was not being able to see Naruto grow-up. Minato then tells her that he of his plan to use Dead Demon Consuming Seal and seal the Nine-Tails into Naruto. She disagrees with him, not wanting to burden Naruto with the Nine-Tails while having no parents to love him. However, Minato, having already made the hand seals and the death god having already appeared behind him, tells her that this is the sake for all shinobi, all the villages, and for Naruto's sake.
Hiruzen and a few other shinobi catch up to Minato, and finds Minato, Kushina, and the Nine-Tails in a barrier. Hiruzen then realizes Minato's plan as Minato seals away half of the Nine-Tails' chakra, causing it to decrease in size. Minato then summons the throne needed for the Eight Trigrams Sealing Style, and places Naruto on it. The Nine-Tails, now aware of what was going to happen to it, attacks Naruto, not wanting to be sealed again. Minato and Kushina both step in front of the attack, causing the Nine-Tails' claw to stop inches away from Naruto, with it stuck in Kushina's and Minato's bodies. While Minato gives Gerotora the key to the seal, Kushina tells Naruto how she wants him to live, and how she loves him. Minato tells Naruto to listen to his talkative mother, then seals the Nine-Tails into Naruto.
After the story, Kushina appologizes to Naruto for forcing him to be the host of the Nine-Tails, and not being there to love him. Naruto expresses no bitterness, accepting the appology and says that he never blamed either of them, now finally understanding the love of a parent's towards their child, and is glad that he is their son. Kushina starts fading away, but before that hugs Naruto and thanks him for allowing her to be his mother, and for allowing Minato to be his father.