Naruto declares to his friends his intention to take on Sasuke by himself, while the Elders of the Leaf make a serious decision about who will fill the vacant seat of Hokage: Kakashi! In Mount Myoboku, Gerotora, Fukasaku and the Great Lord Elder debate whether or not to give Naruto the key to the Tetragram Seal that Gerotora holds, an act that could potentially unleash Nine Tails.
Tsunade sends out Naruto under the guise of a top-secret mission to keep him hidden away from the Akatsuki. Naruto leaves Konoha with Aoba, Yamato, Guy along with three other unknown shinobi. They are however, held up at the pier due to a report of a monster attacking ships causing nobody to want to set sail. When Guy and Aoba go out to see if they can solve the problem, they encounter a giant marlin and a fisherman named Yūsuke who lost his father to the marlin and wanted to avenge him. On the next day, Yūsuke is given a boat and a fishing pole, and after much struggle, he finally catches the marlin with his own strength. After that Naruto and the others finally set sail for the Land of Lightning.
During their voyage, Naruto, Yamato, Guy, and Aoba stop at an island to recover from severe seasickness. There, they unexpectedly meet up with Sakura, Ino, and Chōji who are on an assignment to gather medical herbs for Tsunade. Ninja from the village of Benisu are also collecting medical herbs and have taken almost all of the herbs on the island. After an encounter in a cave on the island were Naruto saves the ninja from Benisu, they decide to give Konoha half of the herbs they collected.
As they continue their voyage towards the Land of Lightning, Naruto, Aoba, Guy and Yamato sail through a thick fog. To pass the time, Yamato tells Aoba and Naruto some ghost stories (much to Naruto's dislike). One of which tells the story of a ship whose crew is comprised entirely of ghosts, which appears in thick fogs such as the one they were sailing through at the time, and can be identified by the flocks of crows that follow it. As Yamato tells the story, a seemingly abandoned ship which meets the exact same characteristics and conditions appears next to their ship. Yamato, Aoba and Naruto board the ship to investigate and Naruto comes across a young boy who says his name is Hishaku. He apparently lived alone on the ship and tended to it but he was once one of the crew of the ship until they were wiped out by a creature Hishaku called the "Skeleton Crab". This creature then attacks the boat, capturing Yamato. Naruto then tells Aoba to warn Guy and the rest of the crew. Naruto, with the help of Hishaku, defeats the Skeleton Crab, and Hishaku then reveals that he is, in fact, a ghost. When the crab attacked the first time, the captain told Hishaku that he was young and to save himself and ever since then, Hishaku's soul couldn't rest, because it felt guilty at letting its crewmates die. When the crab was defeated, Hishaku's soul, and the souls of the rest of the crew members who couldn't rest either, left with the ship, which really was a ghost ship.
On their way to the Land of Lightning, Naruto's ship gets caught in a storm. When the crew gets out of it, they encounter a savage group of pirates, who attempt to sink their boat and capture them. Yamato shields the boat with a Wood technique and they escape underwater in a sub-like contraption, which promptly falls apart. They wash up in an underwater cavern underneath the island the pirates had taken over some time ago. The residents of the island had taken refuge in the caves until they all died. Naruto swears to avenge them all. With a clever plan, Naruto and the ship are rocketed out of the island's dormant volcano top using underground hot springs and he successfully avenges the island folk by defeating the pirates.
Naruto, Aoba, Guy and Yamato continue their voyage towards the Land of Lightning. The episode starts with a storm. During the storm a large bird takes Guy, and when the storm clears up they find an Island. This Island is said to be a summoning island where the large animals such as giant snake, centepede, spider and more live. Aoba saw a girl and tried to pursue her and it leads him to a house where he found a journal about the island. It is said on the journal that they tried to create an ultimate summoning animal. The girl leads Aoba to the research lab in the crater of the volcano where they found the ultimate summoning animal sleeping. Naruto, Guy and Yamato were brought by the large bird to the lab and some of the animals followed them and when the animals come close to the ultimate summoning animal it eats them and assimilates them. It appears that the ultimate summoning animal can use genjutsu and lightning style element. It appears that the girl that led Aoba to the lab is just an embodiment of her thoughts since the girl and the rest of the research team has already been eaten by the ultimate summoning animal. The thoughts of the girl tried to seal the ultimate summoning animal and Naruto used the rasen shuriken to kill the ultimate summoning animal and make it fall into the crater of the volcano.
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.
Naruto's ship stops at a port to resupply, as they prepare to head into the Sea Route of Silence, a stretch of ocean with no wind or fish, which takes two weeks to traverse. On the way, a mushroom Naruto bought from a merchant, which supposedly helps sailors avoid starvation, multiplies in the cargo hold and erodes Yamato's Wood Style chakra, disabling him. Naruto and Guy, after enduring a painfully long time without food, try the mushrooms, which poison them and cause them to act violently. Out of options for food, Naruto has Gamatatsu bring back Shima's meal of insects, which the crew eats, enabling them to survive and defeat a trio of thugs who attempt to raid their ship.
The ship is caught in a storm and Naruto uses his shadow clones to protect the ship.After the storm, Naruto wakes up and a quarrel begins between Naruto and his Shadow clones. Soon his shadow clones revolt and take control of the ship and the crew is forced to land on a nearby island. Naruto is taken hostage by the shadow clones and they put forth their demands to him. Naruto is saved by Yamato and the others only to find that it was a dream. It was caused when a Shadow clone was released and the memories of it returned to Naruto. Naruto then realizes the worth of his clones and releases them.
Shikamaru begins to feel the pressure of shouldering the lives of his friends in the upcoming Fourth Shinobi World War. To help ease his mind, Shikaku sends his son along with Tenten on a mission to Mokuzu Island to replenish supplies. On the island, Shikamaru meets up with Naruto's group. Soon after they set sail, the fog around the area gets thicker and they encounter reef systems, a huge rock and a whirlpools again and again. Shikamaru figures that their ship is sailing through the bay in circles and tells Naruto and the others to sail straight for it and get swallowed up. The Mokuzu Criminal on seeing the ship wrecked arrives at the spot with his gang to loot the wreckage. Having stored the ship in Tenten's scroll, they proceed to defeat the criminals.
Hinata’s father Hiashi summons the Hyuga clan to discuss the role they will be playing in the upcoming Fourth Great Ninja War.
Naruto finds an imposter that has been building his reputation by attempting to steal from other people while his friend is also attempting to gain a reputation by "beating" the imposter up so he builds his reputation even further and become a ninja. Later, mercenaries capture the fake Naruto. The real Naruto then comes and saves the day.
Konohamaru, Udon and Moegi are training to prepare for the upcoming war. After heading to the hospital, Sakura makes them carry and stock boxes. Konohamaru, wanting something more important to do leaves with his team ranting. Shikamaru asks Konohamaru who the "King" was and writes the kanji for King on a stone shaped like a shōgi piece and gives it to him. Konohamaru then goes to see Tsunade who outright says no. Frustrated after seeing Temari who was there to deliver a message from Suna as well as check on the progress of the village after Pain's invasion. Konohamaru later challenges Temari while she is on her way home. The two have an intense spar with Konohamaru being unable to land an attack on Temari. Eventually after Temari taunts him that the Sarutobi clan was left with no good heir and that Naruto had a poor pupil. The two almost end up severely harming each other but the fight is stopped by Shikamaru who had been informed of Konohamaru's intentions by Udon and Moegi. After hearing Moegi's story, Konohamaru realises that the 'King' he wanted to protect were the civilians of the village who were unable to defend themselves. Shikamaru smiles at him and Temari compliments him for mastering such a high-level technique and then Team Ebisu for being such promising young shinobi and then leaves.
A man named Kokuyō wants Shizuka as his wife in order to gain control of her village, a proposition which she repeatedly rejects. Tokiwa, Shizuka's attendant, sees Naruto and tells him he should marry Shizuka if he defeats her, as Jiraiya promised to Shizuka's mother. Naruto declines the offer, but Tokiwa tracks him down and explains Shizuka's past and asks him to reconsider, which he does. He fools Aoba, Guy, and Yamato to buy some time. He defeats Shizuka right before Kokuyō attacks her, only to be defeated by Naruto's Rasengan.
While talking with his students, Shino talks about how he and his team got together and became more close as friends and teammates. The story switches to Shino's flashback during the first part of Naruto. They are on a mission assigned by Kurenai in which a Jonin assassin from a neighboring village. Shino gets defeated because of weak taijutsu and descends into depression. He even reveals he was going to abandon the team that helped him because he didn't think he was useful to them. But after his friends get in trouble with the rouge Shino comes back and defeats the rouge.
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.
Given the day off, Sai spends it strolling the village and drawing. He initially encounters three children that he at first finds it difficult to interact with but later realises that two of them remind him of his team-mates Naruto and Sakura. He has several flashbacks of their time together and the bonds they share. In the end he uses the doors of a destroyed house and paints a mural of Team 7 along with Sasuke holding hands.
As Team Asuma considers the impending war, they encounter Kosuke Maruboshi who reminds them of the time that they rescued him while they were still genin. With this, Kosuke retells the tale of the time their fathers saved him during the Invasion of Konoha with their Formation Ino–Shika–Chō. Somewhat rattled by this story, Kosuke reminds them that great shinobi weren't made in a day. As the team contemplates everything, they decide to perfect their own formation, insisting that they'd be fine because they were not alone.
Kiba becomes upset that Naruto, the dead-last in their Academy days, had become such a hero. After being chided by his mother Tsume and partner Shino, he decided to train in order to become stronger. Seeking out Kakashi, the only available jōnin sensei currently, he asks him to help him train. Kakashi however summons his ninken to aid Kiba and Akamaru in their training. After initially giving up after being defeated by the hounds, Akamaru carries Kiba to a tree in the village where he sees that Naruto had broken his record in speed since the time they were children racing for candy. With his determination renewed, he demands a rematch with the hounds and is successfully able to retrieve the scroll. With this Kiba races to the tree and sets a new record, declaring that he'd never give up.
In the Leaf village, Kakashi while meeting with Tsunade about the impending war, receives an emergency messenger tortoise from Guy with an SOS message, so he heads out to find out what has happened. On board the ship, Guy recalls the time when he and Kakashi first became rivals and their numerous battles since then. Later on in the night, the jōnin meet where Yamato tells them about a rumour of a shinobi capable of not only copying someone's appearance, but also their chakra. Kakashi soon arrives at the ship, and calls for Guy. Unaware that he sent an SOS message, Guy comes to the conclusion that the one before him could be one of those imposters that Yamato spoke of. With this notion Guy proceeds to attack Kakashi and later Aoba and Yamato when they side with Kakashi. After giving Guy irrefutable proof that he was who he said he was by telling him something from their youth, Kakashi returns to Konoha upon learning that the SOS tortoise was sent by accident.
Naruto is almost done with his journey, he only needs to make one more stop for supplies before venturing on. His last stop is on the island, Land of Water. While there Naruto runs into Kurotsuchi and Akatsuchi who are on a mission from the Hidden Stone. Will Naruto help his new friends on their mission, or will he simply continue on his way?