Sasuke and Sai Arc
Yamato was assigned to lead Team 7 in meeting with one of Sasori's spies within Orochimaru's ranks. Naruto and Sakura found it difficult to work with their newest team member, Sai, and much of Yamato's time was spent trying to get them to cooperate. Upon arriving at the arranged meeting place, Yamato went ahead dressed as Sasori, to make meeting with the spy easier. After the spy arrived, who turned out to be Kabuto Yakushi, Yamato was able to learn a great deal of information until Orochimaru showed up. Just as Yamato started to contemplate how he would fight Orochimaru whilst keeping up his act as Sasori, Kabuto cut off the head of the Sasori costume, having hoped to kill the real Sasori.
Faced with a combined attack from Kabuto and Orochimaru, Yamato created a wood clone to escape, causing Orochimaru to realise that one of his test subjects had survived. A battle between Orochimaru and Naruto ensued, and Yamato spent much of his time protecting Sakura. When the battle was over, Sai was found to be missing, although a wood clone that Yamato had following Sai revealed that the latter had joined with Orochimaru. As the clone followed Sai to Orochimaru's hideout, the rest of Team 7 followed the clone. Once they arrived, Yamato used his Wood Release abilities to infiltrate the base. When they eventually found Sai, they restrained him, and were able to learn about Sai's real mission: to join forces with Orochimaru on behalf of his organisation, Root, in an attempt to destroy Konoha.
Sai was eventually freed by Kabuto, who in turn was restrained by Sai. Sai, touched by Naruto's words about Sasuke Uchiha, rejoined Team 7 in their other mission of retrieving Sasuke. When the group split up again, Yamato discovered a Bingo Book whilst going through some of Sai's belongings. In doing so, Yamato learnt that Sai once again had an ulterior motive: to kill Sasuke Uchiha. In desperation, Team 7 went looking for Sai, hoping to stop him from fulfilling his mission. Sai, however, had actually had a change of heart, and attempted to convince Sasuke to come back to Konoha on Naruto's behalf. Sasuke however ended up overpowering Sai.
Due to an explosive attack from Sasuke, Team 7 was able to find Sai and learn that he had really allied with them. Upon failing to persuade Sasuke to return to Konoha, the team decided to use force instead. Sasuke's growth, however, was too much for the four's joint effort, and he was able to repel them all. After a brief confrontation between Naruto and Sasuke, Yamato attempted to capture Sasuke with his Wood Release: Wood Locking Wall, although Sasuke was able to escape. As an answer to this, Yamato declared that he had no intention of getting too rough on him in front of Naruto and Sakura, but had no choice. Despite this, Sasuke prepared what appeared to be a finishing move. Orochimaru and a freed Kabuto arrived to stop him, however, and they disappeared, leaving Team 7 defeated which made them unsuccessful in their mission.
Twelve Guardian Ninja Arc
Yamato led Team 7 on a mission to the Fire Temple. Upon arrival, Chiriku informed them that the tombs belonging to a former member of the Twelve Guardian Ninja had been robbed of its corpse. While Yamato pondered the motive for this, word reached them which had reached the Fire Temple that the graves of three other former Ninja Guardian members had also had their corpses stolen. Yamato, his team, and Chiriku went to investigate and find the four coffins. While Yamato knew it was clearly some sort of trap, he knew they had no choice but to play along if they wished to retrieve the bodies.
As they neared the coffins, the trap was sprung, and the team became trapped in a rocky cavern. While searching for the way out whilst dodging more traps, Yamato was approached by one of the thieves, Fudō. Caught off guard and completely unprepared for an opponent such as this, Yamato was overpowered by Fudō's unique earth-technique prowess and indestructible body, forcing him on the defensive. Eventually, Fudō caught him in a rock-crushing technique, but deceived Fudō by merging with the rocks. Yamato regrouped with his team and, having failed to recover the stolen corpses or capture the tomb robbers, returned to Konoha with Sora.
ater, when the tomb robbers emerged again to attack Konoha, Yamato was one of the few jōnin still available to defend the village. He was then sent out to stop one of the resurrected Ninja Guardians from completing the Limelight technique, but was intercepted by Fudō. After figuring out Fudo's attack patterns, Yamato used Fudō's blunt attack methods to set up the area for a water technique to trap Fudō in mud. He then proceeded to finished off Fudō by crushing him with a wood ninjutsu. He went to join Asuma and the others in stopping the bandits' leader, Furido, who released Sora's Nine-Tailed Demon Fox chakra. Because Yamato's wood release was not as refined as the First Hokage's, he couldn't suppress Sora's spliced demon chakra. Yamato instead used his wood technique to protect his allies from Sora's attacks.
Hidan and Kakuzu Arc
Kakashi recruited Yamato to help with Naruto's training in creating a new technique. In addition to being able to create training devices for Naruto with his Wood Release abilities, Yamato was also able to subdue Naruto if he lost control of the Nine-Tails' chakra. Once Naruto completed the initial stages of his training, he moved onto perfecting his pre-existing Rasengan. Kakashi, however, was not able to oversee Naruto in these final stages, due to his volunteering to help Team 10 in the fight against Akatsuki. As such, he left Yamato in charge of the technique's perfection. Yamato was able to give advice in the technique's creation, and eventually bore witness to the fruits of Naruto's training
Once Naruto had perfected his technique enough to be used in battle, Yamato, Naruto, and the rest of Team 7 joined Kakashi and Team 10. After teaming up with Naruto to stop an attack by Kakuzu, Yamato convinced Kakashi to allow Naruto to fight Kakuzu alone. Once Naruto was successful in defeating Kakuzu, Yamato joined everyone else in returning to Konoha.
Team Kakashi was sent to provide back-up for Team 8 and Kakashi. When they located the team, Yamato assisted in rescuing Hinata. They pursued the opposing Team Guren to a lake, where they located the Three-Tails. The two teams shifted objectives and, once back-up from Konoha arrived, began trying to seal the beast. Yamato was put in charge of a team meant to stop any attempted interference, but ultimately proved unsuccessful. He made a hideout for the teams to regroup in, and later facilitated in Naruto's rescue from the Three-Tails. After another failed sealing attempt, Yamato returned to Konoha with the others.
Itachi Pursuit Arc
When Kakashi received permission from Tsunade to lead a special team to capture Itachi Uchiha in order to bait Sasuke, Yamato joined him as acting head of Team 8, with the pregnant Kurenai remaining behind in the village. Following a confrontation with Sasuke's cohorts in Hebi and members of the Akatsuki, the group was forced to abandon the mission and return to Konoha.
Tsuchigumo Kinjutsu Arc
In the anime, on their way back to the village, Katsuyu appears and gives the team orders for a new mission, to help the Tsuchigumo clan protect their infamous and forbidden technique from being taken by ninja bandits. While Kakashi returns to the village for more information, Yamato is put in charge of the team. Yamato and his team unfortunately arrive at the clan's base too late, as the bandits had already broken through its defences and forced the former clan leader's granddaughter, Hotaru to retreat into the woods. Upon finding her, they discover that she was travelling with a stranger named Utakata who seemed indifferent to Hotaru's well-being as he decided to leave her in Konoha's care. After successfully bringing Hotaru to her village, despite the mission being completed, Naruto refused to leave yet as he felt something was wrong from how the village was so hesitant to let Hotaru return. Upon investigating, it was discovered that the bandits tracked Hotaru down and drove her back into the woods.
While searching for her, they discovered Utakata had returned and was being attacked by Kirigakure ANBU hunter-nin who were holding Hotaru hostage. After managing to calm Naruto down, Yamato tried to talk with the ANBU, explaining the situation and asking them to release Hotaru. The ANBU initially agreed under the condition they hand over Utakata, Yamato refused as he knew Hotaru would refuse to go with the Konoha-nin if Utakata didn't come along. Suddenly, the ANBU's squad captain appeared to make a deal with Yamato, not wanting things to become a war between the two villages. It was then agreed that the ANBU would release Hotaru and not pursue Utakata until the Konoha-nin's mission was complete, as long as the Konoha-nin agreed not to interfere with their pursuing of Utakata afterwards.
Later, the shocking truth is revealed that Hotaru has the clan's forbidden technique embedded in her back. After learning that Hotaru asked for this to help restore the clan, it is acknowledged that the technique will only cause more harm and preparations are made to safely remove the technique from Hotaru's back and destroy it. Not wanting to give up just yet, Hotaru insists they find a man named Shiranami who should be able to help protect the technique, who Naruto goes off to find. Unfortunately, Hotaru runs off when Utakata suddenly leaves. Yamato has Sai track her down back to her clan's village, which has been taken control of by Shiranami himself, who is also the bandit's leader. Yamato and the others arrive in time to hold off the possessed villagers while Naruto and Utakata goes on to save Hotaru.
Invasion of Pain Arc
When the invasion began, Yamato was away on a mission with Sai and Anko Mitarashi, trying to locate and capture Kabuto. Just when they located Kabuto, Yamato detected that Naruto had broken the seal he had placed on the First Hokage's Necklace, and was about to completely release the Nine-Tails. He rushed back to Konoha to try and stop Naruto, but was informed by Shikaku that Naruto was able to suppress the Nine-Tails' power on his own. He was later seen using his Wood Release to help rebuild Konoha, putting a lot of strain on him.
Five Kage Summit Arc
When Naruto states that he wants to meet with the Fourth Raikage, Yamato advises against it; leaving the village is forbidden because of the Kage Summit, Yamato can no longer suppress the Nine-Tails because of the First Hokage's Necklace's destruction, and Yamato needs to help with the village's reconstruction. However, Naruto manages to convince Kakashi, who forces Yamato to go too. Yamato plants a wood clone seed on Team Samui, allowing him, Naruto, and Kakashi to follow them to the Raikage in the Land of Iron. When Naruto is unable to sway the Raikage, the three of them rest at a local inn. Tobi confronts Naruto while there and Yamato and Kakashi, having expected him, try to restrain him. Their attempts do not work and, after telling them the truth about the Uchiha clan and Sasuke's current motives, he leaves.
Yamato repairs the damage he and Kakashi did to the inn. Soon afterwards Sakura arrives with Sai and tells Naruto that she loves him, shocking Yamato. He tries to ask why she would say that, but was stopped by Kakashi before he could. As he watched and listened to Sakura's talk to Naruto, he could tell she wasn't being sincere, and like Kiba, looked upon it both questioningly and disapprovingly. She leaves when Naruto says he doesn't believe her, after which one of Sai's ink clone's approaches them and tells them Sakura's plans to kill Sasuke. Before Kakashi can go to stop her, Gaara appears and tells them about the outbreak of the Fourth Shinobi World War and Danzō Shimura's actions during the Kage Summit. Because the other Kage would prefer Kakashi were Hokage, Yamato encourages him to comply. Naruto passes out shortly afterwards and Yamato is left in charge of looking after him while Kakashi finds Sakura.
When Naruto finally awakens, he tries to go after Sakura, but Yamato stops him and insists that they return to the village. Naruto asks to rest some more and Yamato lets him, unaware that Naruto is sneaking out, leaving a shadow clone behind so that he wouldn't notice. In the anime, it is shown that after realising that Naruto had escaped he hunts him down to the Samurai Bridge and captures him, but later releases him and returns to the village on his own.
Adventures At Sea Arc
Yamato is assigned to a team consisting of Aoba, Might Guy, Naruto, himself, and three unknown shinobi to travel to the Land of Lightning to confine Naruto in an isolated location in preparation for the Fourth Shinobi World War. Tsunade ordered the team to take the longer route to the Land of Lightning, so they head to the Land of Fire's harbour. While there, they are warned by fellow Konoha shinobi about a sea monster. After choosing a small inconspicuous boat, the team is attacked by the sea monster, which turns out to be a Giant Marlin that was summoned during the Third Shinobi World War. As Naruto helps Yūsuke, a fisherman who was attacked by the marlin, and is left open, Yamato shields Naruto from the attack as Aoba distracts the marlin, which allows them to escape.
Back at Yusuke's hut, the Konoha shinobi are told by Yūsuke that he want's to avenge his father who had died trying to capture the fish by capturing the fish himself. After Naruto says he wants to help Yūsuke, everyone agrees and Yamato creates a new boat and fishing rods.
As the team sails through a thick fog, Yamato tells Aoba and Naruto about the "Ghost Ship" to pass the time but suddenly meet another ship that fits the description of the "Ghost Ship". After exploring the ship, they come across Hishaku and his crew, who are revealed to be "souls" who cannot rest because of guilt about their ship being attacked by a Giant Corpse Crab. After defeating the crab with the help of his team, setting the ship free, they continue sailing.
Yamato's team is later attacked by pirates who want to sink their ship and loot the wreckage but thanks to Yamato's fast thinking and the early warnings by one of the sensor-type shinobi, the ship was saved.
Yamato is seen again with Naruto on an island searching for Guy, who had been kidnapped by a giant bird. After searching the island and encountering many giant creatures they find Guy babysitting the bird's chicks. The bird takes Naruto, Aoba, and himself to the volcano where they encounter Aoba and a beast who goes on a rampage. Yamato then protects Naruto while he enters Sage Mode and defeats the beast.
The group stops for supplies to prepare for an area devoid of fish that takes two weeks to cross. Yamato's chakra is absorbed by a poisonous mushroom that Naruto purchased which multiplies and fills the boat. As the mushrooms cause Naruto and Guy to act in a violent manner, Naruto asked Gamatatsu to bring them some of Shima's food, which helps them regain the strength needed later to defeat the pirates that sold Naruto the mushroom.
Confining the Jinchūriki Arc
In the anime, Yamato is seen in a bar with Shikamaru, telling him that since the First Hokage's Necklace was destroyed, he could no longer suppress the Nine-Tails. Yamato is one of the Konoha ninja sent to an isolated island in the Land of Lightning as Naruto's bodyguard. When Naruto expresses an interest in finally taming the Nine-Tails, Yamato and Motoi accompany him to the Falls of Truth in order to defeat his dark side. After a brief encounter with the Giant Squid again, B instructs Naruto on how to enter into his subconscious and face the Nine-Tails. When the Nine-Tails starts gaining the advantage and a chakra cloak develops around Naruto, Yamato tries to suppress it. It eventually stops on its own, surprising him. Naruto soon informs them of his victory, explaining the particulars to B through a fist-bump. Being left out of the loop irritates Yamato, but he is left amazed when Naruto begins demonstrating his new control over the Nine-Tails and the advantages it allows him. Among the advantages is the ability to sense Kisame hidden within B's Samehada. Naruto pursues Kisame when he tries to flee, but his inexperience with his new strength and speed causes him to lodge himself in the wall. Yamato helps Naruto while B goes after Kisame.
Yamato splints Naruto's sprained ankle and warns him to exercise restraint until he can gain better control over his powers. They rendezvous with B and find that Kisame has been captured. Yamato fortifies Kisame's wooden restraints while Aoba Yamashiro reads his mind. Before Aoba can learn anything of real value about Akatsuki, Kisame breaks free and commits suicide. They try to examine the intel Kisame wanted to escape with, but it is booby-trapped and they are trapped in water prisons while the the intel makes its way to Akatsuki.
Fearing that Naruto may grow suspicious about their reasons for being on the island given his dominance over the Nine-Tails and the incident with Kisame, Yamato and the others convince him to take a survey of the island's native animal population to keep him busy. Akatsuki, meanwhile, launches an assault on the island, and Yamato looks after Naruto and formulates explanations for any signs of the battle that Naruto notices. When things calm down, Yamato, Aoba, and Motoi go outside to investigate. They come across Kabuto as he is captured by Kurotsuchi. Yamato creates a wooden beam that Aoba can walk on to approach Kabuto and read his mind like he did with Kisame, but Kabuto sheds his body to free himself. He goes after Yamato and, before being captured, Yamato pushes Motoi out of the way.
Kabuto escapes to the Mountains' Graveyard where he and Tobi gather information from Yamato about the Allied Shinobi Forces. Kabuto also studies Hashirama's DNA within Yamato to strengthen the White Zetsu Army. Rather than kill Yamato when he has fulfiled his usefulness, they suspend him opposite Hashirama's clone for future use.