Part I:
When Team 10 and Naruto Uzumaki were given a B-rank, potentially A-rank, mission of rescuing the son of a daimyō, Shū, who was an ally to the Land of Fire, Tsunade called for Yamato. Because of rumours about there being suspicious activity going on in the Land of This where Team 10 was heading, she had Yamato secretly tail the younger Konoha-nin in the event things became S-rank danger and also gather any information possible. Later, after Team 10 completed the initial phase of their plan, capturing Shū, the nation was suddenly attacked by Akatsuki. Yamato took action and destroyed several of Sasori's puppets. Despite his help, the nation ultimately fell to the Akatsuki's attack. With Team 10's mission still going to return Shū home, Yamato tailed them until they crossed the country borders. Afterwards, Yamato returned to Konohagakure to report to Tsunade, who became troubled by the news.
Part II:
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 fached 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.
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.
Three-Tails Arc.
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.
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 was alerted to the fact that Naruto had broken the seal he had placed on the First Hokage's Necklace, and was about to completely release the Nine-Tails with a seal appearing in his palm with the number of tails that Naruto had manifested. 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: Serial Pillar Houses Technique to help rebuild Konoha, complaining that it put 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, even with his and Kakashi's support, 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. However, as the event unfolds an angered Yamato 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 telling the truth, 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.
Confining the Jinchūriki Arc.
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.
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