Sakura sees Sai drawing by the river and finds out that Sai has artistic talent but has never given titles to anything he ever drew. Naruto and Sakura begin to realize the reason behind Sai's repulsive personality. After the hot springs, the team heads off to the bridge to meet the spy. Yamato is suspicious of traps so they go off the main road into the forest. Camping for the night, Yamato then creates a two story house by again using his Mokuton jutsu. Inside this house, the team formulates their plan.

Kabuto creates a fake corpse that resembles Sai, containing hidden traps to slow down Yamato's clone after sensing it. Naruto hasn't completely recovered from using the Demon Fox's chakra, and Yamato says that he will be left behind if he cannot keep up. Naruto is determined to finish his mission and not slow the team down. However Team Kakashi is forced to take a break when it's clear that Sakura has not fully recovered from her own injuries. Yamato then uses this opportunity to talk to Naruto alone and reveals to him that the one who hurt Sakura was Naruto himself. Naruto is shocked by what Yamato says to him.

As Team Kakashi continues their search for Sasuke, Sai approaches Sasuke's room and awakens him. Shaken by the image of Sasuke's Sharingan from earlier, Sai attempts to restrain him. A large explosion occurs and Sakura, Naruto and Yamato catch up. At first Sakura tries to restrain Sai in order to find out his true objective, but she stops, stunned at seeing her former comrade. Contrary to what the rest of the team assumed to be his mission, Sai tells them that he wishes to bring Sasuke back to Konoha.

With Konoha in complete darkness, the village struggles to defend against the four attackers who have sealed the entire village behind a barrier. The entire village is in a state of emergency. Asuma, commanded by Tsunade to follow Sora and Naruto, finally catches up to them. Asuma realizes that the four invaders plan to annihilate the entire village using the lightning powers of the corpses that they stole. The revelation shocks Sora. As Asuma leaves to help hold off the attackers, he instructs Naruto to continue pursuing Sora.

Team Asuma continues their battle with Akatsuki's Hiden and Kakuzu.

Shikamaru continues his fight with Hidan. Hidan manages to injure Shikamaru and curses him the same way he did Asuma, but when Shikamaru survives Hidan's attack, Hidan realizes something isn't quite right.

While Naruto continues his training with Gamakichi and Gamatatsu, Yamato, Sakura, and Sai prepare to leave and back-up Kakashi's group. As Guren and her gang prepares to intercept Kakashi's group, Yukimaru grows concerned for her safety and gives her a charm in hope of a safe return.

Naruto runs into Guren while trying to find Yūkimaru. Yamato and Kakashi find Naruto and bring him back to the group. Kabuto tells Guren that Yūkimaru is only a tool to control the Three-Tails, which upsets Guren. Meanwhile, Shizune, Ino, Tenten and Lee meet up with the team and tell them that their new mission is to rescue Yūkimaru and capture the Three-Tails before Orochimaru's group can capture it.

Kabuto plans on breaking Leaf’s The Four-Corner Sealing Barrier from the inside by using Yukimaru’s power and have the Three-Tailed Beast go on a rampage.

Guren tries to attack Naruto within the Three-Tails, but, in her weakened state, is unable to do so and passes out. Meanwhile, Kakashi tells Sakura and Ino to heal Yūkimaru while he, Shizune, Kiba, Sai, and Hinata search for Naruto. Naruto and Guren soon encounter a horde of mini Three-Tails that try to attack them, but they evade them and begin to argue about Yūkimaru. While Yūkimaru awakens, Naruto summons a bunch of Shadow Clones to look for a way out of the beast's stomach. Elsewhere, Kabuto gives Curse Marks to Rinji's men.

While the members of Team Hebi head towards Itachi's location, Jiraiya infiltrates the Hidden Rain Village in hopes of gathering information on the Akatsuki leader. Jiraiya captures two Rain ninja and interrogates them about Pain, but what he learns shocks even him.

After successfully breaking out of Itachi's Tsukiyomi, Sasuke gains the upper hand on his weakened brother. With no other alternative, Itachi activates his second Mangekyo ability, Amaterasu, a black flame said to burn forever.

After failing to bring back Sasuke, the Leaf ninja start heading back to the Hidden Leaf Village. Tsunade, however, sends Katsuyu to inform them that the barrier of Mount Katsunagi of the Tsuchigumo Clan, which holds a powerful forbidden jutsu, is broken. While Kakashi and Team 8 head back to the Leaf Village, Team 7, lead by Yamato, must check out what events are taking place.

After the peformance of the forbidden jutsu, Hotaru is horrified to see the damage the jutsu has done. Shiranami then notices the forbidden jutsu overflowing with chakra and the fact that it would destroy itself along with Hotaru. While Naruto chases the fleeing Shiranami, Utakata tries to save Hotaru using the hidden power within him. Can Utakata save Hotaru?

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.

As the ninja of the Hidden Leaf Village work on repairing their village in the aftermath of Pain's invasion, Naruto and Sakura come across a familiar face among the carpenters: Inari and Tazuna have arrived to help out. Inari recalls what happened after Gato's death and how Naruto and Sasuke came to his rescue.

Back before Rock Lee had his surgery, Naruto, after donning the suit given to him by Guy, set out on a mission with Sakura and Ino to obtain a special flower which was a necessary ingredient for Lee's medicine. When Naruto picked one of the flowers, however, he had to face a strange technique that had taken on the form of Gaara.

A female spy, Hanare, from the Hidden Lock Village (Land of Key) is caught by ANBU pretending to be a musician. She is interrogated. However, the interrogation proves unsuccessful. Slowly, her past is revealed and so is her relationship with Kakashi. Team 7 spy on the two as they go around town, under the impression that the two are dating. After The Lock Village keeps a Leaf Village ninja hostage, they exchange Hanare for the ninja. It is then revealed that Hanare has a special ability, causing a large chase to occur. In the end, Kakashi lets Hanare free. The musician seen at the beginning entertaining Konoha ninja reminds Kakashi of Hanare which prompts the flashback.

Karui decides to get information about Sasuke from Naruto by any means necessary. When Naruto refuses to sell Sasuke out, Karui takes out her frustration upon the former. Meanwhile, Danzo prepares for the Kage Summit, and determines to keep Naruto confined to the Leaf Village.

One of Sai's clones tells Naruto the truth surrounding Sasuke, something that Sakura couldn't bring herself to do. Before Naruto can even comprehend what Sai just said, they are interrupted by Gaara. What additional bad news concerning Sasuke does Gaara bring for Naruto?

Naruto returns to the Leaf Village, and his teammates demand to know why he didn't finish Sasuke off when the latter was in such a weak state. Naruto tells them that when the time is right, he will deal with Sasuke personally. Meanwhile, a supposedly deceased member of Akastuki has infiltrated the Hidden Cloud Village.

Tsunade sends out Naruto under the guise of a top-secret mission to keep him hidden away from the Akatsuki. Unfortunately, Naruto, Yamato, Gai, and Aoba are stuck at the pier due to a report of a monster attacking ships.

Shikamaru begins to feel the pressure of shouldering the lives of his friends in the upcoming Fourth Shinobi World War. To help ease his mind, Shikaku sends his son along with Tenten on a mission to Mokuzu Island to replenish supplies.

With Killer Bee as his new master, Naruto begins his training to control the power of a Tailed Beast. In order to do so, one must fight the Tailed Beast head on and absorb its chakra, converting it into one’s own power.

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.

During their battle against the White Zetsu, Shino’s beetles detect the presence of another enemy. Leaving the fight to Kiba and the others, Shino goes to investigate and finds Torune preparing to unleash his forbidden jutsu.

Naruto uses up the last of his chakra trying to free the Tailed Beasts from Madara’s control. When all seems lost, the Nine Tails finally acknowledges Naruto as its jinchuriki and offers its help.

Having absorbed the chakras of all nine Tailed Beasts, the Gedo Statue begins its transformation into Ten Tails. Naruto, Killer Bee, Kakashi, and Guy try to destroy the Gedo Statue but are stopped by the masked man.

Ten Tails is on the brink of its final transformation and begins to form a massive Tailed Beast Bomb.

Naruto's power of persuasion moves Obito's heart. Due to the influence of the Ten Tails, visions of himself and Rin from the past appear in the inner realm and play havoc with Obito’s emotions.

Madara has transformed into the Jinchuriki of the Ten Tails and appears before Kakashi. Kakashi and the others combine their powers to attack, but they are no match for Madara..

Guy activates the Eight Inner Gates Formation and relentlessly attacks Six Paths Madara. Even Madara, who has attained power strong enough to create huge fissures in the ground, tries to dodge Guy's direct attacks.

Naruto joins up with the rest of his comrades, and together they overcome the puppet attack. The masked man witnesses this and is convinced there is a future for the young shinobi. He promises to release the kidnapped jonin and begins to explain the truth, and the situation behind his motives.

"The fourth Great Shinobi World War has ended. But Sasuke decides to continue his solitary journey—this time to atone for his sins. Meanwhile, back at the Leaf Village, there is a growing number of missing shinobi. As Kakashi—the sixth Hokage—and the others discuss these incidents, the Leaf is attacked by a mysterious group of shinobi."