The movie revolves mostly around a special mineral called the Gelel Stone, which has a strong and mysterious power. There was once a clan that could control the stone’s powers, but they were destroyed because of wars for the stone.
A battle was taking place at night on a desolate seaside beach between Sunagakure ninja and soldiers wearing bulky suits of armour. Despite their best efforts, the Sand ninja are slowly overwhelmed by the sheer strength of their mysterious opponents. The timely arrival of reinforcements, led by Kankurō and Gaara, turn the tide of battle, with Kankurō slicing apart a suit of armour with his puppet, and Gaara dispatching a large number of enemies with his signature Sand Waterfall Imperial Funeral. However, when Gaara orders the Sand-nin to shine a flare at the retreating enemies, a large warship is revealed, with its own arsenal of heavy weapons, much to the Sand shinobi’s shock and curiosity of its appearance. The ship then opens fire with its guns, and Gaara’s sand armour barely manages to protect his comrades as its artillery shells relentlessly pounded the beach.
Naruto Uzumaki, Shikamaru Nara, and Sakura Haruno are on a mission to capture a lost pet ferret and deliver it to its village. Naruto comically refers to the creature as a cat for the remainder of the movie. But while on their way to return the animal, they are attacked by a mysterious man clothed in knight armour. He too is accompanied by the strange armoured soldiers from before. The three fight him, but get separated when Naruto, the knight and the pet ferret all fall off a cliff. Shikamaru and Sakura only realise afterward what has happened and immediately go to look for them. Before they can, what appears to be an earthquake stops them in their tracks until they realise that it isn’t an earthquake at all, but the movement of a giant mechanical moving structure. Sakura and Shikamaru split up to search for Naruto.
Naruto wakes up to find himself bandaged, as well right next to an equally wounded unknown man. They have been taken in by a very peaceful caravan of nomads that own a number of foreign animals, including ostriches and rhino. An old man goes on to inform Naruto that they are in fact the village that hired the leaf ninja to return their pet ferret, named Nerugui. The ferret also seems to have a great interest on the unknown man, much to the despair of the elder. While healing, the man seems to have a flashback dream that depicts what happened to him as a child. His home was invaded and destroyed while he hid, seemingly the only one alive. He is almost found, but in the last moment he is spared and manages to live.
Kahiko and his granddaughter Emina goes onto explaining to Naruto how their clan once originally had a country, but it was destroyed a very long time ago by some kind of disaster, and that Nerugui is proof of it. They also tell him how Nerugui is in fact older than the clan elder, having been looked after by the clan for generations. As Naruto looks for an explanation from Temujin, the knight only asks Naruto about his strange ‘power,’ that is actually his chakra. Temujin appears not to know what chakra is, even if he can wield a similar power. Temujin simply tells him that he is there ‘to build a utopia,’ then goes on to invite Naruto to join him. Naruto promptly refuses, only for the ostrich he is riding to run away on its own.
Still looking for an explanation from Temujin, Naruto follows him as he sneaks away from the caravan. After risking his injuries to save one of the caravan’s children from falling from a tree, Temujin claims that his debt has been ‘repaid’ and continues to leave.
Meanwhile, Shikamaru infiltrates the mechanical structure and finds what appears to be a lab with children in capsules. They are overlooked by a pair of women (Kamira and Ranke) with similar armour to what Temujin had been wearing, whom operate a machine that makes the bulky soldiers from before. The two discuss the Gelel Stone, something that Shikamaru has never heard of. He is almost caught, but manages to flee at the last moment.
Naruto discovers that Temujin has gone missing and goes to head after him when Kahiko comes to him, saying how Nerugui has disappeared again. As his mission was to deliver the pet to the village the group was headed to, he still has to complete it. The clan elder even goes as far as saying he should have hired the Sand Ninja instead. Even though he returned the ferret to its owners, Naruto still must go and find it again. Meanwhile Sakura comes across an abandoned campfire and finds the caravan’s trail.
Naruto goes on to find Temujin again, who has Nerugui with him. (He comically tells him to hand over the ‘cat.’) Temujin finally reveals his name, as they find themselves in front of the large vessel from before. They go inside, revealing the structure to be very advanced in technology and sort of like a European cathedral on the inside. There, Temujin introduces Naruto to his master, Haido. Dressed in what appears to be bishop robes, Haido goes on into detail about their goals, and again extends the invitation to join them. Naruto claims that he can’t join them because he’s going to be Hokage, but offers to spread the peace that they wish for. Nerugui appears on Temujin’s shoulder, instantly showing a dislike for Haido. Haido starts thinking when they mention a caravan.
They move out when an overhead announcement tells them that the fleet that was sent to the Land of Wind has been annihilated. Temujin and Naruto head on to find the ship that had attacked the Sand Ninja, beached with all kinds of metal parts in the sand. Once they investigate the vessel, Naruto discovers Kankurō among a room filled with unconscious children amongst all of the rubble. Kankurō immediately attacks Temujin, explaining how the ship had been wiping out Land of Wind villages. Naruto demands an explanation, but all Temujin can reply is ‘Noble sacrifices for the greater good.’
Before they battle, they are interrupted by the Kamira and Ranke, whom Kankurō and Gaara take on. Kamira uses a kind of mind control that seems to be genjutsu. Meanwhile, Ranke transforms herself, causing her to have several gorilla-like traits, as well as large lightning attacks. After a hefty battle, Gaara manages to distinguish Ranke’s lightning and kill her, but Kamira manages to flee by growing bat-like features, wings included. During the commotion, Naruto is separated from Temujin.
The movie shifts to the caravan being attacked by one of Haido’s followers known as Fugai. After destroying most of the wagons and killing most of the livestock, she questions Kahiko about where the Gelel stone is. Thankfully who should step in but Shikamaru and Sakura, who claim to have seen her flare. They already managed to take out the soldiers. Fugai goes on to take on wolf-like traits and manages to escape. Shikamaru questions the elder about the Gelel stones, but the he doesn’t want to talk. They start to leave, saying that they need to find a friend. When Kahiko asks if their friend is Naruto, they find out that Naruto was with him. The elder goes on to ask the two for help.
Through a series of flashbacks, we discover how Temujin met Haido after his village was destroyed. We also discover that Temujin actually has a Gelel stone inside of him, causing his eyes to appear the red colour they are. After getting word that the caravan from before has information, Temujin returns to what is left of it only to be captured by Shikamaru. Naruto has managed to find Shikamaru and Sakura, and the three stay with the caravan people, who had managed to escape and are currently hiding in a cave. There, they question Temujin to find out what Haido wants with the Gelel stone. Kahiko claims that the stones only cause harm, but then Temujin reveals how he has a stone inside of him.
The elder goes on to question Temujin about a book and about their clan, confusing Temujin. He tells them that only members of the royal family of their clan could bind the stones with their bodies, Temujin being one of them. He then tells them that the royal family left and crossed the ocean, taking the Book of Gelel with them. Temujin hasn’t come to a new land, in fact he has returned home. Kahiko tells them that they don’t know of the stone’s origin, but they do know it was a mineral that their clan was able to refine and use as they pleased. It was very powerful, so much that an entire civilisation was wiped out in a battle over it. Afterward the few remaining clan members sealed it away in attempt to keep it from happening again. The only reason they didn’t destroy it was because the only ones who could were those of royal blood.
Determined after the tale, Temujin tells them that he only wants to achieve his dream of a utopia. He manages to escape (he was free the whole time) and kidnaps Kahiko to make him lead him to the Gelel mines. They don’t know where the mines are, but Nerugui manages to lead them to it. Temujin and the elder find the ruins and journey deep into them to find the entrance to the mines.
The Leaf ninja try to save Kahiko, only for Haido and his entourage appear. Shikamaru tries to stop Haido to question him, only for Haido to claim he only wants peace, and he’s going to create a utopia. Shikamaru ironically states that they are doing the exact opposite. Naruto angrily asks him if he even cares about his fallen comrades, whom Haido only claims are ‘noble sacrifices.’ Temujin grimly agrees.
After Naruto tells them that dreams without friends are nothing, the elder finally triggers a mechanism that seals him and Temujin into a passageway into the mines. Haido reveals that he possesses the Book of Gelel before smashing Naruto into the wall like it was nothing and follows them. Kamira and Fugai attack, but Shikamaru and Sakura hold them off to allow Naruto to follow Haido.
Temujin and Kahiko find themselves in the ‘Chamber of Sealing’ and find a picture that appears to be one of despair. The elder tries to reason with Temujin, but Temujin doesn’t wish to hear it. Kahiko then reveals a knife.
Meanwhile, Kamira toys with Shikamaru as she flies around, he is unable to get a lock on her shadow. But then he suddenly spots Kankurō on the far side of the ruins. As Fugai chases after Sakura, she is unable to lose her even after Sakura blinds her. Finding a crystal structure that creates echoes, Sakura uses herself as bait so Fugai will howl and triggers the crystals to collapse on top of her. Shikamaru fills the whole area with lines with explosives (most of them are fake just pieces of paper) so Kamira cannot fly about. Just as Kamira thinks she knows what he has in store, Kankurō suddenly launches one of his puppets to automatically trap and kill her.
After wounding Temujin, the elder has his blood on a dagger that he tries to pierce a seal on the floor, only for Haido to interrupt. Just as Haido finds the mine’s key, Nerugui tries to stop him. The ferret is killed by a barrier around him, a Gelel stone falling out of the ferret’s mouth. Temujin stands in front of the elder as Haido is about to kill him, Temujin claiming there is no reason to kill him. Temujin suddenly has a bit of deja vu, just as Naruto appears. Haido tells Temujin to kill the both of them, but Temujin has had enough and refuses. Haido then claims that he is useless, no different from his parents. Deja vu happens again, and Temujin finally realises that Haido was the one who murdered his parents.
Haido goes on to turn into his own kind of creature, then captures Temujin and extracts the Gelel stone from him. The elder begs Naruto to stop Haido. Naruto encourages Temujin to get up as he fights, even going so far as to use Rasengan. But Haido has managed to tap into the mine and heals all of his twisted limbs. Naruto still wishes for Temujin to help him, and just as Haido goes to finish them, the fake soldiers go and protect them both. The souls of the children emerge as the soldiers are destroyed, and Temujin finally realises his wrongdoings.
Combining both Rasengen and the Galel stone, Temujin and Naruto manage to to kill Haido. But in the process they accidentally destroy the key to the mine. The walls start to crumble around them as the mine spirals out of control. Shikamaru, Sakura and Kankurō all manage to retrieve the children from the machines, only for the ruins to start collapsing. They cannot control it, but there is a way to destroy it. If Temujin puts his hand on the seal from before, he can summon a time/space continuum. Only royal blood can do it, and the one who does will end up sacrificing himself. Naruto tries to stop Temujin from doing it, for Temujin to knock him out. He says doing it is the only way to atone for what he’s done. Temujin goes into the collapsing Galel to the seal and activates it.
All is quiet as Shikamaru, Sakura, Kankurō and Gaara can only watch as everything in the void’s way begins to be devoured. Naruto remembers Sasuke as he is faced with Temujin’s death. As Temujin waits for his fate, suddenly he finds himself floating as a line of Naruto clones have clutched onto him. Sakura almost goes into the void herself to see where Naruto is.
Only at the last moment a burst of the Gelel escapes and causing the land mass to start moving. When it finally stops, they find Kahiko, who claims that he feels even better than ever thanks to the Gelel. He is even joyously reunited with a still alive Nerugui. The wastelands have now turns into an oasis, as all the children awaken.
Temujin awakes, realising he’s still alive with Naruto still clutching his arm. They find picture from despair from before, and it wasn’t one after all, in fact it was one of hope.
Later they all gather at the ocean, where Temujin and the others all gather and prepare themselves to leave, back to the land that they came from. They are aware that it’s one with lots of conflict, but Temujin wishes to help where he can. Temujin’s eyes have now turned back to their original bright green. And much to the elder’s disappointment again, Nerugui has chosen to go with them as well. As they leave, Naruto stands on a cliff and shares a sign with Temujin, promising each other never to give up.