After a long voyage at sea, Naruto’s ship finally arrives at the island of its destination. Before everyone can rejoice, a giant squid attacks the ship. Fortunately, the crew is saved by Killer Bee, the Eight Tails’ jinchuriki host.

Motoi confesses to Naruto and Yamato that he attempted to kill Bee during their childhood because of his father's death due to the sealing of the Eight Tails 30 years ago.

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.

Inside his mind, Naruto continues his battle against Nine Tails to take control of its immense power.

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

Minato is forced to use his Flying Raijin jutsu and leave his wife Kushina behind to save their newborn son, Naruto, from a masked assailant.

I ninja della Foglia riescono a respingere la Volpe nella foresta grazie al Terzo Hokage Sarutobi Nonostante Kushina sia inizialmente contraria, Minato spiega che per proteggere il villaggio, e così anche suo figlio quello è l'unico modo poiché la volpe non può restare senza un Jinchuuriki o si creerebbe uno squilibrio, convincendo cosi Kushina definitivamente. I due decidono di sigillare anche le restanti parti del loro chakra dentro il figlio per poterlo rincontrare in futuro, in particolar modo Kushina sperava di vedere il figlio cresciuto. Proteggendo Naruto un'ultima volta da un enorme artiglio del Kyuubi che trapassa entrambi, Minato prima di morire attiva il Sigillo del Diavolo, i due genitori salutano il loro bambino augurandogli una vita felice. Al termine del racconto, Kushina svanisce abbracciando suo figlio ringraziandolo.

Essendo ora in grado di utilizzare il chakra della Volpe, Naruto riesce a scoprire Kisame nascosto dentro Samehada. Il ninja di Alba riesce a fuggire con un rotolo contenente le informazioni ricavate, ma Gai si lancia all'inseguimento e attiva la settima porta del chakra. I due si scontrano sulla costa utilizzando le loro tecniche più potenti: Gai ricorre alla Tigre di mezzogiorno e Kisame allo Tecnica del mega proiettile marino. Inizialmente, il colpo di Kisame sembra avere il sopravvento, ma Gai riesce a colpire il suo avversario.

Dopo essere stato sconfitto da Gai, Kisame viene bloccato dall'Arte del legno di Yamato. Aoba entra nella mente del ninja e assiste al ricordo di un giovane Kisame facente parte della squadra d'intelligence del Villaggio della Nebbia, ma con la missione di impedire la fuga di informazioni anche a costo di eliminare i suoi compagni. Anni dopo, per ordine del Mizukage, Kisame uccide il suo maestro, spia del villaggio, prendendo la spada Pelle di Squalo. A quel punto, interviene il Quarto Mizukage Yagura che, però, è controllato da Tobi. Prima che Aoba veda Tobi in volto, Kisame si risveglia e, pur di non rivelare nulla al nemico, si uccide lasciandosi divorare dagli squali da lui stesso evocati. Il rotolo con le informazioni raccolte viene recuperato, ma si rivela una trappola ed Akatsuki ottiene la posizione del Kyuubi e dell'hachibi (novecode ed ottocode).

Tobi heads to Hidden Rain Village to retrieve Nagato's Rinnegan. Konan, now a former member of Akatsuki, recollects her past until Tobi arrives. Tobi asks Konan where is Nagato's Rinnegan and Konan replies that it is not located in the village. Their battle started and Tobi tells Konan that he encouraged Yahiko to form Akatsuki and he gave the Rinnegan to Nagato. Konan transforms into thousands of pieces of paper to self-destruct against Tobi, yet it fails and both survives. Konan unleashes a powerful paper technique that looks like a sea of paper beneath their feet.

Konan encloses Tobi in an chasm with a large amount of explosive tags that detonates in a wide area. Tobi manages to survive with his Izanagi techique, sacrificing one eye, and pierces Konan behind. Tobi explains his technique to Konan. Konan refuses to give up and continues to fight Tobi. Tobi manages to subdue her and places Konan inside a genjutsu to force her to reveal the location of the Rinnegan. Tobi travels to the location and retrieves Nagato's corpse and then takes his leave. A bloodied piece of paper is blown of Konan's body by the wind and travels to her childhood hideout. As it travels, more of the Ame Orphans past with Jiraiya is revealed, as well as some of their time as the original Akatsuki. Meanwhile, Tobi, with a new outfit, is told by Zetsu that they have received intel on the Nine-Tails wherabouts from Kisame. He declares that it's time to capture the Nine-Tails.

Zetsu reports on new intel from Kisame and Madara learns about Naruto hideout. Tsunade, Gaara, Lord Raikage, and others must figure out how to get Naruto out of the secret island of Land of Lighting and all without telling him about the war. New mission is introduced.

Kabuto and a reanimated Deidara attempt to grab hold of the jinchuriki, but are stopped by the Tsuchikage, who has come to protect Naruto.

Fourth Great Ninja War is about to begin, ninjas are going through their formations, medical supplies are being checked and restocked. The title of this Naruto Episode is "Assemble Allied Shinobi Forces". The headbands are done. Let's go! Tsuchinage saves Nine Tails and Eight Tails, but Yamato gets captured.

Part Two of the Four Week Long Special Project for the Broadcast's Tenth Anniversary - During the Chunin Exam, Sasuke witnesses Naruto’s growth as a shinobi.

Part Three of the Four Week Long Special Project for the Broadcast's Tenth Anniversary - Sasuke’s defeat to Gaara, and later Itachi, forces him to realize that he is not strong enough to get revenge against his older brother.

Part Four of the Four Week Long Special Project for the Broadcast's Tenth Anniversary - Naruto is determined to save Sasuke, who has deserted the Hidden Leaf.

The Allied Shinobi Forces are on standby, ready to confront Madara’s army of reanimated shinobi and 100,000 White Zetsu. But distrust still exists among the Allied Shinobi Forces, who were once sworn enemies until recently.

Kankuro’s commando unit enters enemy territory to set up a stronghold for the Allied Shinobi Forces. They are immediately ambushed by the Akatsuki’s own commando unit comprised of the reanimated Deidara and Sasori.

The Allied Shinobi Forces’ commando unit engages with the Akatsuki in the first wave of battle.

Under the guidance of Killer Bee, Naruto enters the final stage of training to master the Tailed Beast Bomb, a Jinchuriki’s most powerful technique.

The commando unit is in hot water as they engage the reanimated Kekkei Genkai shinobi, which include Zabuza Momochi and Haku. Luckily, Kakashi and his unit arrive in time to assist them.

Kakashi and his unit devise a strategy to take on the Kekkei Genkai shinobi, but it’s foiled by Kabuto, who uses the Reanimation Jutsu to summon the most powerful members of the Seven Ninja Swordsmen of the Mist.

The Akatsuki dispatch an army of powerful reanimated shinobi and White Zetsu across the war zone, causing chaos within the Allied Shinobi Forces’ chain of command.

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

Atsui, Samui, and Darui face off against Kinkaku and Ginkaku, the legendary brothers from the Hidden Cloud, feared even by the Raikage.

Darui manages to seal away Ginkaku. Fueled by the rage of losing his brother, Kinkaku transforms into a monster that resembles a jinchuriki’s Tailed Beast State.

Ino sees Sakura falling from the sky. Although she manages to save her, the shock of the fall has left Sakura with amnesia.

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

The Ino-Shika-Cho trio is ordered by Shikaku to take down the reanimated Asuma. Remembering Asuma’s final words, Shikamaru and Ino are determined to stop their former teacher.

Choji is unable to attack Asuma and loses his will to fight. Ino and Shikamaru try to snap Choji out of his paralysis.

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.