Plot
Yamato, Naruto Uzumaki, Sakura Haruno, and Sai are assigned on a mission to capture Mukade, a missing-nin. They all have chakra-knives, which are uniquely designed trench knives that allow a ninja to infuse their chakra with it to produce an added effect. They set out for the once glorious historic ruins of Rouran, a city with one thousand towers and is located in the middle of the desert. They pursue and corner the missing-nin. Mukade's goal is revealed to travel to the past and take over the Five Great Shinobi Countries with the power of the Ryūmyaku, an ancient chakra flow deep underground Rouran. He unleashes the power of the Ryūmyaku, which is seen to have been sealed by Minato Namikaze (who was well known as Konoha's Yellow Flash), causing a light to envelop Naruto and Yamato, who was trying to stop Mukade. Sai stops Sakura from getting sucked in by the Ryūmyaku by grabbing her onto his ink bird and flies to safety, leaving Naruto and Yamato in the mysterious light. Naruto and Yamato are sent twenty years into the past. When Naruto awakens from this time slip, he meets the queen of Rouran, Sāra.
It's later revealed that Mukade traveled to the past 6 years before Naruto did. By this point he has changed his name to Anrokuzan and serves as the minister of Rouran. He has killed Sāra's mother Sēramu, the previous queen, and is now attempting to kill Sāra and take over the world. Naruto tells Sāra that he will protect her. Anrokuzan appears to have slaves - who are citizens of Rouran - who do his dirty work. With the Ryūmyaku, Anrokuzan is able to create the "Puppet Ninja Forces", which can attack using the Ryūmyaku's chakra, and are able to use weapons such as kunai and deflect attacks. (Naruto is seen using his chakra-knife to attack them.)
Minato Namikaze is now seen at Konoha, and Jiraiya shows Minato that he has completed the Rasengan. Then the young Shizune, Maito Gai, Asuma Sarutobi, and Kakashi Hatake are waiting in a long line at the grand opening of the Ichiraku Ramen Bar. Hiruzen Sarutobi has heard of Anrokuzan's evil plans, and sends Minato Namikaze, Shibi Aburame, Chōza Akimichi, and upon Minato's request, Kakashi Hatake, to put an end to his plans. Naruto later comes into contact with Minato, who is now on his mission. Minato tells Naruto that he too is a Konoha ninja, and tells him to go back to his own time period, as it's not safe at Rouran. He then tells Naruto the circumstances at Rouran, and gives Naruto his hirashin kunai to hold on to. While Minato is talking to Naruto, Sāra has a flashback of when she was a little kid and her mother. They were singing until Anrokuzan came and stabbed Sēramu, while Sāra ran away.
Later Anrokuzan is seen to be a giant puppet, he is able to use parts of the towers of Rouran to repair himself from any attack, which is part of his regenerative technique with the power of the Ryūmyaku. Naruto goes up against Anrokuzan in a battle using his Shadow Clone Jutsu, Rasengan and Wind Style: Rasenshuriken, but fails. Naruto's out of chakra, having no way to fight him, Naruto is left defenseless. Minato then comes and saves Naruto and by lending Naruto his chakra the Rasengan was formed in his hand and at the same time Minato forms a Rasengan as well. By having similar chakra, their chakras resonate with each other growing more powerful by the second. They then combine their Rasengan to form the legendary Super Rasengan. Sāra seals off most of the Ryūmyaku, making Anrokuzan unable to use his regenerative technique. Minato goes off and exposes Anrokuzan's weak spot, then tells Naruto that this is the time to attack him. Naruto succeeds in hitting him with the Super Rasengan. Anrokuzan states that this is not be over. As the floor crumbles, he falls down into a pool of the Ryūmyaku. Sāra is still seen on the crumbling floor, Naruto manages to catch her, but falls in too. Yamato, who is holding on to Kakashi, comes and uses his Wood Style to catch Naruto. Minato asks Naruto to give back his kunai to completely seal off the Ryūmyaku. A bright blue light shines as Minato seals the Ryūmyaku. Naruto and Yamato's bodies begin to glow. Minato says since that Anrokuzan is dead, his spell, which made them travel to the past, wears off. Minato decides it's best to have all of everyone's memories erased in order to not to change history. Naruto tells Minato that they still need to talk, and that if he doesn't now he'll never have the chance to. As Minato begins placing a seal, Naruto begins to realize something, but was interrupted by Minato's reply that if he ever has a son he wishes that he be brought up as a ninja like Naruto (having realized that Naruto was his future son). Sāra tells Naruto that she'll never forget what Naruto had taught her.
Naruto and Yamato's bodies completely fade away. In the present time, the Ryūmyaku that is unleashed by Mukade fades away. Sakura is still seen on Sai's ink bird crying out Naruto's name. Sakura and Sai retrieve Naruto and Yamato, who don't seem to remember the events that had just transpired.
As they wander outside, Naruto and the group run into someone who greatly resembles Queen Sāra - she says that she'd felt a disturbance in the Ryūmyaku, pulling out the chakra blade that Naruto had given to Queen Sara during the events of the time slip. It is nicked and damaged, as if it had been through twenty years of use. Naruto, recognizing the blade, instinctively reaches for the sheath on his back, but of course, he does not have the blade. The girl says that it was a blade given to her mother by a 'hero in a dream,' and that the will of her mother lived on in her as she strives to protect her people.
As she walks away, Naruto is contemplative, and comments that she reminded him of someone he'd met before. Sakura then grabs and pulls on Naruto's ear and yells at him for having 'perverted daydreams.'
