Celý tým v doprovodu mnichů doráží do chrámu Ohně. Naruto je šokovaný, protože stejné místo viděl i ve svých snech. Sora, mladý adept na mnicha, neustále Naruta provokuje a rozčiluje. Ten si však všímá, že mniši mají na Soru stejný pohled, jako mívali obyvatelé Konohy na něj. Snaží se k Sorovi přiblížit a stát se jeho přítelem. Vzápětí však přichází zpráva, že byly vykradeny další hrobky.

Zombie armáda útočí, aby odvedla pozornost od hlavního plánu nepřátel. Asuma, který má zlou předtuchu o tom, co se tu doopravdy děje, se vydá k elektrárně, kde se jeho podezření potvrdí. Čtyři z jeho přátel z doby, kdy patřil mezi Strážné nindži, jsou oživeni a nuceni použít techniku na vyhlazení celé Konohy. Mezitím, co Naruto bojuje se ženou, která dokáže ovládat všech pět elementů čakry, se snaží Sora zjistit skutečný důvod útoku na vesnici.

Chiriku byl zabit a Akatsuki nesou jeho tělo na výměnné místo, kde za něj dostanou peníze. Ve chvíli, kdy se zpráva o jeho smrti dostane do Konohy, Tsunade okamžitě svolává nově vytvořené týmy. Za úkol dostávají zajmout nebo zabít členy Akatsuki. Mezitím Naruta pohání jeho odhodlání mílovými kroky kupředu a konečně se mu podaří splnit druhý krok k vytvoření nové techniky.

Tým 10 se vydává na cestu za dvojicí členů Akatsuki. Narutovi a Sakuře je dovoleno jít za nimi, pokud Naruto dokončí svou techniku do 24 hodin. Mezitím Shikamaru plánuje strategii a líčí ji svým společníkům. Akatsuki zapečetili dvouocasého démona a Hidan s Kakuzem míří do Konohy pro tělo Asumy a pro Naruta. Ino je pomocí své techniky sleduje v těle orla. Když dorazí Hidan a Kakuzu na místo, začíná bitva.

Kabuto vezme Yuukimara na jezero, kde uvolní jeho sílu a ověří tím, že v jezeru žije stvoření, o které mají zájem. Kakashi posílá pomocí Pakuna vzorek krystalu do Konohy na analýzu. Naruto vzdává společný trénink s Gamariki a přivolá si Gamakichiho a Gamatatsa. Bohužel, výsledek je stále stejný. V lázních Naruto potkává Yuukimara. Po Yuukimarově odchodu následuje rozhovor, ve kterém mu žáby vysvětlí pravou podstatu jeho tréninku.

Sanbi není snadným protivníkem ani pro Orochimarovi spojence. Kabuto však nemá v plánu se vzdát. Okolo jezera se rozprostřela mlha způsobující iluze. Konožtí se dozvídají o Sanbim a Tsunade okamžitě vysílá pečetící tým. Yuukimaru má obavy o Guren a její vzpomínky nám mezitím odhalují původ rudých kamélií. Naruto se také nemůže smířit s tím, že má svého nového kamaráda nechat napospas Kabutovi, Guren a Sanbimu.

Všechny Deidarovy pokusy zabít svého protivníka selhaly a Sasuke navíc Deidaru vytáčí čím dál tím víc. Proto se Deidara uchýlí ke své poslední možnosti. Sám sebe promění v obrovskou bombu, která má Sasukeho určitě zabít.

Jsou přivoláni další dva Peinové. Každý z nich ovládá jednu techniku a všichni tři sdílejí pohledy. Stačí, aby jeden pozoroval mistra, a vidí ho všichni. To si jeden ze tří Legendárních sanninů uvědomil a v sennin módu pokračuje v boji. Pomocí Fukasakiho a Shimina genjutsu se mu podaří zabít všechny své protivníky. Nastal ale nečekaný zvrat událostí. Všichni tři mrtví byli vzkříšeni a Jiraiya znovu stojí proti nepříteli. Tentokrát však proti všem šesti Peinům.

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

Udon, Moegi a Konohamaru mají za úkol pomáhat při evakuaci vesničanů. Konohamaru narazí na jednoho z Peinů a ten si ho všimne. Mistr Ebisu chce odlákat pozornost, aby mohl chlapec utéct, je však chycen. Konohamaru ho osvobodí a podaří se mu použít Rasengan, čímž Peina zastaví. Naruto přijde na způsob, jak sbírat energii za běhu.

Sakura reflects upon a time when she was infected with a strange disease by Naruto. In order to find a cure, an order was issued for Naruto to be quarantined at all costs before he could infect anybody else.

Might Guy recalls their "visualization" training with Lee in order to avoid learning the Drunken Fist and forgetting an incident which Might Guy apologizes to the restaurant owner with humiliation. Lee, who is determined to train to be stronger than Naruto, follows Might Guy's orders and resemble animal fighting styles which represent on a restaurant menu. However they failed, until they tried on training on a moving boat. Like Guy who has seasickness, Lee also suffers from seasickness but he uses it to balance the boat which resembles exactly as the Drunken Fist fighting style. Guy lately realizes that Lee is also aware of the restaurant incident and Lee was only protecting Guy from a drunk man which causes the restaurant to be totally damaged.

Tenten remembers when she was little and how she really wanted to become like the legendary Tsunade. She finds out through hard training that she won't be capable of the strength Tsunade has. She also finds out that she won't be suitable to be a medical ninja for her poor chakra control. But at last, she discovers that she has the ability to summon ninja tools, thus creating her own style of fighting.

Sixteen years ago, Fourth Hokage Minato Namikaze and his wife Kushina are expecting their first child, much to the delight of the young couple.

As Darui and his First Company engage an army of White Zetsu, the remaining forces must deal with reanimated shinobi.

Kankuro’s Commando Unit is cornered by Hanzo’s poison attack. Fortunately, Mifune and his Fifth Company arrive in time to provide assistance.

While training in Chakra Mode, Naruto senses the presence of the Nine Tails’ chakra seeping from Kinkaku outside. Curious to find out what’s happening, Naruto tries to leave the training room when Iruka suddenly steps in to stop him.

Over at the Medical Unit camp, Sakura and the other medic ninja work nonstop to treat the wounded. Neji is there to recover from overusing his Byakugan.

Tsunade and the Raikage arrive to prevent Naruto and Killer Bee from joining the battle. But the two Kage fail to convince the Jinchuriki to turn back, forcing the Raikage to use extreme force.

Gaara leads the Fourth Company into battle against the previous Kage, including his father, the late Fourth Kazekage. The Fourth Kazekage attacks Gaara in order to determine if his son is truly worthy to be the current Kazekage.

Naruto and the others finally regain their lost memories regarding Yota. Years ago, the Leaf Village kids came to befriend Yota, but the adults believed the young boy was a spy and took him away for questioning.

Naruto and Killer Bee take on the six Reanimated Jinchuriki, who’ve been equipped with the Rinnegan. Using his past experience from fighting the Six Paths of Pain, Naruto devises a plan to stop the Jinchuriki.

Kabuto attempts to bring Sasuke over to his side by pointing out that they both are fighting for the same goal: to bring down the Leaf Village. But Sasuke quickly rejects him.

Thanks to Itachi, the Reanimation Jutsu is released, and all the Reanimated Shinobi are returned to their resting places. But to everyone’s surprise, the real Madara still remains!

Obito watches in disbelief as Kakashi kills Rin. Unable to accept the harsh reality, Obito decides to carry out Madara’s dream so that he can create an ideal world where Rin still exists.

Orochimaru is forced to flee the Hidden Leaf after Third Hokage Hiruzen exposes his illegal experiments. Danzo, fearing that Orochimaru’s capture would lead to the exposure of his own involvement in the experiments, sends out one of his men to help.

Itachi Uchiha is inducted into Kakashi’s unit as the youngest member of the ANBU Black Ops. Itachi’s father, Fugaku, is pleased, thinking this will grant the Uchiha access to exclusive, top-secret Leaf intel.

Kakashi desperately tries to reach out to Obito, but his words fall on deaf ears. Obito instead accuses Kakashi of being trash, which angers Naruto, forcing him to step in and defend his Sensei.

The Senju and Uchiha clans join together to build a shinobi village and fulfill their dreams.

Team 7 is finally reunited when Naruto, Sakura and Sasuke join forces.

The Ten Tails morphs into its final form, "The Divine Tree," and attacks the shinobi, absorbing their chakra one after another.

All the Tailed Beasts are freed, and old friends Kakashi and Obito come face to face with each other. What will Obito's response be? Meanwhile, the Tailed Beasts and the Allied Shinobi Forces shift their focus onto their greatest foe, Madara Uchiha. Gaara is reunited with his former Tailed Beast, Shukaku. When Gaara asks Shukaku to lend his power to seal Madara, he refuses. Will their history of animosity prevent them from working together?

When Hinata is labeled unfit as a successor, Hanabi's heart becomes bound to her destiny.

Neji and the team come across Matsuri collapsed in the desert and find out that Gaara is in danger. Meanwhile, the chains of a mysterious priest bind Gaara and Foo.

It’s been three years since Naruto set out to train with Jiraiya, and he's just returned to the Hidden Leaf Village. Konohamaru immediately begs Naruto to teach him a new jutsu and he starts to go over the basics...but his explanations are very vague. Soon after, Naruto sets out on a mission, leaving Konohamaru to figure it out alone!

Tenten falls under the Infinite Tsukuyomi and wakes up in the Hidden Leaf Village. When Lee and Guy Sensei appear, Tenten is relieved to see that she is not alone. But her joy is short-lived, as both men act oddly and are dressed stylishly—just where has she been transported to?

Tsunade continues to read Jiraiya’s novel. Chunin- and jonin-level ninja have gone missing, and the Fourth Hokage, Minato, orders a search mission with teams of genin led by Guy and Kurenai. Kakashi’s Team 7 is also dispatched, but the hero Naruto Uzumaki, despite being the Hokage’s son, has the misfortune of being labeled a loser.

Sasuke has left with Orochimaru, but Naruto is not about to give up. Determined to bring Sasuke back, he returns to the village with Shikamaru and the others. Meanwhile, Yahiko appears in the village, calling himself “Pain" and seeking revenge for the Hidden Leaf’s betrayal.

Seeing Hinata almost die triggers Naruto’s anger and he goes into Nine Tails State. Naruto's power is enormous, but Pain releases his jutsu to seal him away. Hatred consumes Naruto as he tries to break the seal. With Naruto unable to calmly control the Nine Tails’ power, the village steadily heads toward destruction.

Itachi becomes a rogue ninja and joins the Akatsuki. He is welcomed and introduced by Pain and Orochimaru as the ex-Leaf ANBU and the man who massacred his entire clan. Itachi is paired up with a man named Juzo, and their first job together is to fulfill an assassination request in the Land of Water.

The Infinite Tsukuyomi does not affect Hashirama, Tobirama, Hiruzen and Minato because they are reanimated. Hagoromo, the Sage of the Six Paths, appears and explains to the four that Hashirama and Madara are the reincarnations of his sons Ashura and Indra. Hagoromo recounts the tale of how he founded Ninshu, the Ninja Creed, and about the lives of Ashura and Indra.

Chakra—whose energy connects this world to those beyond—allows Obito to leave Rin's side for a moment and appear in Kakashi’s inner psyche. Obito gives him his Magekyo Sharingan and leaves with a parting wish that Kakashi become the Sixth Hokage.