The film concerns the potential outbreak of a Fourth Shinobi World War when ninja with kekkei genkai abilities begin to disappear from Kumogakure, Iwagakure, Kirigakure, and Sunagakure.
Team Kakashi is sent on a mission to follow the tracks of the missing kekkei genkai-wielding ninja, which leads them to Mount Shumisen, located between the Land of Earth and Kusagakure. Sai, who is flying on his ink bird, is attacked by a bird which attacks with explosive tag-like feathers. Naruto, disobeying Kakashi's orders to continue the mission, runs towards where Sai fell, saying he will not abandon Sai. There, chimera-like creatures attack them which they quickly defeat, although Naruto is injured in the process.
Back at Konoha, Kakashi gives a report on the mission to Tsunade, while worrying that the next ninja targeted will be him. Tsunade seems to not care so much, telling Kakashi to relax. At the hospital, Kakashi gives Naruto his bells, which they used for their first drill together, and tells him to fix them because he crushed them.
Konoha ANBU are sent to Mount Shumisen by Tsunade to search the area for tracks of the missing kekkei genkai ninja. There, a mysterious ninja along with his followers, absorb their chakra with his mysterious technique using their Earth nature affinity against them.
That night, the same mysterious ninja, the mastermind and antagonist of the film known as Hiruko, projects his image over the skies of the Five Great Ninja Villages, introducing himself as a shinobi of Konohagakure. He states that he has taken the kekkei genkai of the four missing ninja using the Chimera Technique, and that he plans to gain the fifth and final kekkei genkai which will make him immortal. By doing so, he declares the Fourth Shinobi World War. Konohagakure is believed to be behind the incident, as by the way Hiruko introduced himself, it seems that Konoha is using or working with Hiruko. Rumours circulate that they are preparing a rebellion. With the other nations amassing troops at the Land of Fire's borders, threatening invasion, the Fire Daimyō orders Tsunade to apprehend those who are responsible and prove Konoha's innocence; in the event of failure, the Land of Fire will be forced to destroy the village in order to preserve world peace.
Tsunade is awaiting Gaara at a secret meeting place to discuss what shall be done. However, on the way there Gaara and his Sunagakure shinobi are attacked by a bird-like creature, which traps them in an avalanche.
Meanwhile, Hiruko states that the Chimera Technique alone can only absorb a maximum of four kekkei genkai, and that certain conditions, most importantly the light af an annular eclipse, which is two days away, is required for the absorption of the fifth and final kekkei genkai, which will make him immortal. That night, Hiruko appears before Kakashi in a dream, activating a Puppet Curse he had placed on him over ten years ago, planning to steal Kakashi's Sharingan. Kakashi asks Tsunade to allow him to go, for the sake of the village. Before he leaves, Kakashi asks Tsunade to place a special seal on him which will automatically activate Kamui when Hiruko attempts to absorb him.
The same night, Shikamaru is visiting Asuma's grave while Kakashi is visiting Obito's. Kakashi asks Shikamaru to tell Naruto that he is leaving the village, and not to follow him. As Kakashi lets Hiruko take over his body, Naruto sees him and chases him. Shikamaru stops him and tells him what Kakashi told him to say. At the Hokage's office, Tsunade orders the Konoha 11 to stay away from Kakashi, labelling him as a missing-nin for the sake of the secret mission. After the others leave, Tsunade tells Nara Shikamaru the truth, trusting that he will do what he needs to do as the leader. Meanwhile, Sakura comes to rescue Naruto from the cell that Shikamaru put him in, then they leave the village to rescue Kakashi. The Konoha 11 are sent to retrieve them.
The next day, Sunagakure is lining up troops and weapons at the borders of the Land of Fire, thinking that Konoha attacked Gaara, their Kazekage.
When Naruto and Sakura follow Kakashi, the Konoha 11 meet with them, and try to bring them back. Naruto reveals what Kakashi once told Team 7 during their bell test: "It is true that in the world of ninja, those who break the rules and regulations are regarded as scum, but those who abandon their comrades are even worse than scum," which changes the minds of some members. However the scene is interrupted by Ichi, who was sent by Hiruko to stop and/or delay them, using his chimera snakes. Team Guy stays behind to allow the others to pass through the first gate.
Ni and her chimera nin-dogs stop them at the next gate, and Team 8 stays behind to delay her, while Naruto and Sakura, and later Team 10, pass.
As Naruto, Sakura, and Team 10 reach the next gate, San appears riding the bird that fires exploding feathers. Team 10 is still following the original mission, and tries to stop Naruto and Sakura. However, Sai appears on his ink bird, using a flash bomb to create a distraction, and takes Naruto and Sakura with him, leaving Team 10 behind to fight San.
At this point, Rock Lee and Neji defeat Ichi using Front Lotus: Eight Trigrams Palms Revolving Heaven while Tenten distracts him, and Team 8 defeats Ni using Secret Technique: Insect Sphere inside a trap that Shino built while Inuzuka Kiba and Hyuga Hinata delayed her. Team 10 gains an advantage over San, with Shikamaru binding him with his shadow and Ino using the Mind Body Switch Technique to take over his mind to tell him that they are after Naruto, not Kakashi. They also ask him where Kakashi is headed. However, San breaks out of the Mind Body Switch Technique. He then summons Ichi and Ni, uses the Chimera Technique on them and himself, and the three become a huge chimera, which seems to be a combination of all their respective chimera beasts, possessing all of their abilities.
Meanwhile, Gaara is thinking of what Jiraiya said while aiding in the recovery of Gaara and the Suna-nin. He has told Gaara that he believes Kakashi, or even Naruto, will defeat Hiruko, and it is up to Gaara depending on whether he believes in Naruto's strength or not. As the war between Konoha and Suna is about to begin with ground combat troops and heavy artillery from both sides facing each other, Jiraiya appears above Gamabunta and gives to Suna the proof that Gaara is still alive. At that moment, Gaara moves to where Naruto, Sakura, and Sai are headed and stops them. He says Naruto's will is not what Kakashi wants, and Naruto begins to fight Gaara. Gaara states that Naruto is too idealistic, and that he doesn't have the power to make his goals become true. However, Naruto strongly says by the belief that as a fellow comrade, he cannot allow Kakashi to sacrifice himself. Naruto breaks through Gaara's Shield of Sand, and punches him.
The rest of the members of Konoha 11 arrive to aid Team 10, and they bind the chimera beast, with the help of Tenten, by sending their chakra to the chains that were holding the beast, they asked Shikamaru to go and stop Naruto, Sai and Sakura. Shikamaru meets Gaara, who tells him that he felt what Naruto feels in the battle. Shikamaru continues on. Meanwhile, Naruto reaches the final gate, and realises this is the place they came to on their past mission. Naruto goes to Kakashi and tries to stop him, but Kakashi walks on with no response. When Naruto grabs his arm, he sees the seal on his wrist, and Sai tells him what it is. Shikamaru, who has finally caught up to them, reveals that Tsunade placed the seal on him, so that they may defeat Hiruko at the sacrifice of Kakashi. Kakashi passes through the final gate before the temple.
As Naruto, Sakura, Sai, and Shikamaru approach the temple, Naruto hears Hiruko's voice, and questions why he did this, and Hiruko answers by telling his story. He claims to have been a former friend of the Sannin, but he was not a skilled shinobi like they were. He was developing the Chimera Technique, a jutsu that would allow him to create a synthetic body by combining several separate ones. After the Third Shinobi World War, he was shocked when he saw Kakashi, not only because he had survived the battle, but because he had received the Sharingan, a kekkei genkai, from the original user, Uchiha Obito. This gave Hiruko the idea to steal kekkei genkai to become powerful like the Sannin. However, the Hokage found out about his research, and Hiruko was forced to flee.
As Kakashi reaches the temple, Hiruko appears from the shadows of the temple, and welcomes Kakashi. Seeing it as the only way to save Kakashi, Naruto, Sakura, and Sai try to defeat Hiruko although Shikamaru tries to stop them. Hiruko, using his four kekkei genkai: Storm Release, Dark Release, Steel Release, and Swift Release, defeats them with little effort. He then steps into the temple with Kakashi. Naruto stands up, deciding that he cannot give up. Shikamaru tries to stop him, saying that he must protect the unborn children of Konoha, the "King". Naruto states that he'll protect them too, and that he loves Konoha for its shinobi, who will sacrifice themselves to save one another. However, deciding who will be sacrificed from the start isn't what Naruto wants, and Naruto believes there is no future for the children if Konoha becomes a place like this. As Naruto walks away, Shikamaru sees Asuma in him, and protects him from surrounding barrier tags with his Shadow Sewing Technique. He states that Naruto has inherited the Will of Fire, trusting the future of Konoha to him.
Naruto enters the temple, where Hiruko begins the absorption at the beginning of the eclipse. Suddenly, Kakashi's Mangekyō Sharingan activates, and the space inside the slime created by the Chimera technique begins to distort. Naruto, trying to save Kakashi, creates shadow clones and breaks into the slime with multiple Rasengans and pulls him out. Kakashi wakes up, asks Naruto why he is here with him and then sighs that the plan failed. Hiruko is still alive, and he states that the eclipse hasn't ended yet, and releases a large amount of chakra, reducing the surrounding area to rubble. When Hiruko summons the chimera beast that the Konoha 11 were keeping restrained, Shikamaru, Sakura, and Sai fight the beast while Naruto and Kakashi face Hiruko. Shikamaru notes that Hiruko's weak spot is his chest, which is still hollow as it is the space that Hiruko wants to assimilate Kakashi into. As the chimera beast begins to gain an advantage over them, the other Konoha 11 arrive to help.
Chōji uses his Multi-Size Technique to become a giant and attacks the beast, followed by Kiba and Akamaru's Fang Passing Fang which destroys the beast's wings, then from the sky, Hinata and Neji appear and attack the beast with the Eight Trigrams Sixty-Four Palms. Lee kicks it into a mountain and Tenten finishes it off with her Twin Rising Dragons, covering its body with a large number of kunai with explosive tags attached and detonating them. Meanwhile, Hiruko is gaining an advantage over Naruto and Kakashi, easily absorbing their techniques: the Big Ball Rasengan and Lightning Cutter. Hiruko gives Naruto a taste of his own attack - Rasengan and returns Kakashi his Lightning Cutter. As a last resort, Naruto forms the Wind Release: Rasenshuriken, and carries the impact to Hiruko's chest. Hiruko tries to absorb and copy it, but cannot combine the high level of shape manipulation with the high level of nature transformation. As the Rasenshuriken's impact occurs, the chimera dies as Tenten makes her explosive tags explode.
In his final moments, Hiruko, in his original form, asks Kakashi what he did wrong. Kakashi tells him that he used others to overcome his weakness, and only tried to become perfect himself. Hiruko says that is the way the strong ones think, and that he did not have any comrades. Suddenly, Hiruko sees his old friends Tsunade, Jiraiya, Orochimaru, the Third Hokage and some others appear before his eyes, and they tell him that they were there for him. Kakashi tells him if he had tried to bond with them, they would've helped him and he shouldn't have tried to do everything by himself. Hiruko then tells Kakashi that was what Kakashi tried to do this time, abandoning his comrades. Kakashi says that he and Hiruko made the same mistake as they were both lost. Hiruko asks him if he has finally made a connection, and dies. Kakashi looks over to see most of the gang cheering for Naruto. He then says that Naruto had long surpassed him.
Gaara appears before the Suna-nin army, and tells them everything has been solved, and to withdraw. Tsunade and Jiraiya talk about how they have been saved, and that the kids are completely different than they were at their age. They end the conversation with a conclusion that they are getting old, and a decision to leave the future in the hands of young generation in which they can freely put their faith into.
The movie ends at Mount Shumisen with Kakashi thinking about Obito. He smiles at Naruto after seeing the similarities between the two. Naruto takes the smile as something creepy and random. The Konoha 11 surround them on various parts of the rocky ledge, each give their input on Kakashi's sexual orientation upon seeing this. Kakashi hurriedly denies their assumptions but not before Naruto panics and flees from him. Kakashi then chases after the fleeing Naruto trying to explain himself.
- Junko Takeuchi as Uzumaki Naruto
- Chie Nakamura as Haruno Sakura
- Satoshi Hino as Sai
- Kazuhiko Inoue as Hatake Kakashi
- Nana Mizuki as Hyuga Hinata
- Kosuke Toriumi as Inuzuka Kiba
- Shinji Kawada as Aburame Shino
- Ryoka Yuzuki as Yamanaka Ino
- Shotaro Morikubo as Nara Shikamaru
- Kentaro Ito as Akimichi Choji
- Koichi Tochika as Hyuga Neji
- Yoichi Masukawa as Rock Lee
- Yukari Tamura as Tenten
- Akira Ishida as Gaara
- Romi Park as Temari
- Yasuyuki Kase as Kankuro
- Hochu Otsuka as Jiraiya
- Eisuke Asakura as Teuchi
- Haruhi Nanao as Nohara Rin
- Hidekatsu Shibata as Sarutobi Hiruzen
- Jurota Kosugi as Sarutobi Asuma
- Keiko Nemoto as Shizune
- Masako Katsuki as Tsunade
- Noriaki Sugiyama as Uchiha Sasuke (flashback)
- Sosuke Komori as Uchiha Obito
- Tomohiro Tsuboi as Kozuki Izumi
- Tomoyuki Kouno as Hagane Kotetsu
- Hideo Watanabe as San
- Kanji Suzumori as Taiseki
- Junko Minagawa as Ni
- Yoshimitsu Shimoyama as Ichi
- Soichiro Hoshi as Hiruko
- Maile Flanagan as Naruto
- Kate Higgins as Sakura
- Dave Wittenberg as Kakashi
- Ben Diskin as Sai
- Stephanie Sheh as Hinata & Rin
- Kyle Hebert as Kiba
- Derek Stephen Prince as Shino
- Colleen O'Shaughnessey as Ino
- Robbie Rist as Choji
- Tom Gibis as Shikamaru
- Danielle Judovits as Tenten
- Brian Donovan as Rock Lee
- Steve Staley as Neji
- David Lodge as Jiraiya
- Liam O'Brien as Gaara & Kotetsu
- Michael Lindsay as Kankuro
- Tara Platt as Temari
- Debi Mae West as Tsunade
- Megan Hollingshead as Shizune
- Patrick Seitz as Ichi & Teuchi
- Richard Cansino as Izumo
- Doug Erholtz as Asuma
- Steve Kramer as Hiruzen
- Vic Mignogna as Obito
- Yuri Lowenthal as Sasuke
- Matthew Mercer as San
- Kirk Thornton as Taiseki
- Laura Bailey as Ni
- Todd Haberkorn as Hiruko
- The movie's poster, along with the 10th Anniversary logo, can be seen after the opening in Naruto Shippuuden episodes 113, 118, and 121.
- The theme song for the movie is "Dareka Ga" aka Someone Is (誰かが) by Puffy AmiYumi.
- The film's soundtrack was release on the late Michael Jackson's 51th Birthday; August 29, 2009.
- It was the only movie that Naruto did not use the chakra of the Nine-Tails or even mention it. However, Sakura did comment on how fast Naruto healed as usual.
- This is the first movie in which there is no new variation of the Rasengan. He does however for the first time make a perfect Rasengan without a Shadow Clone's aid; instead using both hands to form it.
- When Naruto used the Rasenshuriken technique on Hiruko, he doesn't get isn't exhausted and his arm doesn't get damage.
- Naruto inherits Kakashi's bells which are the ones used to test the three young gennins when they first meet Kakashi.
- Pakura, Toroi, Gari and Chūkichi, who were introduced in the manga as part of Akatsuki's army bear striking resemblance, in appearance, clothing, and village affiliation to the kekkei genkai-wielders abducted by Hiruko, having different kekkei genkai, or in Chūkichi's case, no kekkei genkai.
- In this movie, flashbacks to Kakashi during the Third Shinobi War depicted Kakashi as still having his White Light Chakra Sabre still intact and being able to activate and deactivate his Sharingan eye.
- The requirements for Hiruko to fully absorb each stolen kekkei genkai, "heaven", "earth", and "human", might be a reference to "Escape Techniques" (遁術, Tonjutsu), on which nature transformation techniques in Naruto are based. They're divided in three groups: "Ten Methods of Heavenly Escapes" (天遁十法, Tenton Jūhō), "Ten Methods of Earthly Escapes" (地遁十法, Jiton Jūhō), and "Ten Methods of Human Escapes" (人遁十法, Jinton Jūhō). All are also collectively known as "Five Escapes, Thirty Methods" (五遁三十法, Goton Sanjūhō).
- Hiruko is the first villain in any Naruto movie to show any remorse for his past actions before his death.
- According to the calender in Tsunade's room, this movie takes place between the 6th to the 9th of an unknown month.
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