Sai and Sasuke Arc
During Sakura's battle with Sasori, she learned of a spy in Orochimaru's inner circle, an opportunity for them to find Sasuke after his years of absence. Kakashi was left hospitalised from overuse of the Mangekyō Sharingan, soYamato was assigned to lead Team Kakashi in his place. Sai was also added to the team as Sasuke's replacement, but neither Naruto nor Sakura were able to accept him as such.
In route to the meeting place with the spy, Yamato tried to get the team to work together, although Sai's personality and disdain for his predecessor caused only conflict amongst the team. When they arrived at the meeting spot, they found that the spy was Kabuto. Yamato, disguised as Sasori, spoke with him, but they were interrupted by the arrival of Orochimaru. Kabuto, in turn, turned against Yamato, who was forced to call Naruto and the others for back-up. Surprised to see Naruto, Orochimaru wondered aloud if Naruto had become as strong as "his Sasuke". Enraged that Orochimaru had spoken as if Sasuke belonged to him, Naruto entered his three-tailed form, and attacked him.
While a fair match, Orochimaru was able to evade Naruto's attacks. Further provoked by his inability to land a debilitating blow, Naruto advanced to his four-tailed form, losing his sense of self in his anger. Now a danger to Orochimaru, Naruto was forced back so that he could switch targets, his first being Sakura. Yamato restrained him before he could do any real harm, and forced the Nine-Tails' influence to recede. When he woke up, they found that Sai had joined up with Orochimaru. They followed him in the hopes that he would lead them to Sasuke, and to see what he was up to. During a break, Yamato took Naruto aside, and told him of how he had attacked Sakura, encouraging him not to rely on the Nine-Tails if he really wanted to protect those close to him.
When they arrived at Orochimaru's hideout, they infiltrated the lair, and captured Sai. Exposed, Sai revealed that his superiors had sent him to help organise another invasion of Konoha. He was restrained for his treachery, while the others went looking for Sasuke. Sai, having earlier met Sasuke, asked why Naruto was so determined to bring him back. Naruto explained that the two had a bond that couldn't be broken, and that he would risk his life to protect this bond. Intrigued, Sai switched sides, helping them to capture Kabuto and then scouring the base in order to reunite Sasuke with Naruto. He succeeded, but was attacked by Sasuke, the magnitude of which drew the rest of Team Yamato to their location.
Together again, Naruto and Sakura tried to convince Sasuke to come home. Still determined to gain power, he refused, prompting the team to use force. Their efforts were unsuccessful, and Naruto, who was exhausted from his fight with Orochimaru in his four-tailed form, wasn't able to compete with Sasuke's growth. Within his subconscious, the Nine-Tails began to offer Naruto its chakra, but he firmly rejected its assistance. The Nine-Tails became contemptuous at Naruto, mocking him that if it wasn't for its power, he would be nothing. It then tempted Naruto to break the seal so it can "grant" him all of its power, but he still refused. However, before their quarrel could escalate any further, Sasuke with his Sharingan activated, suddenly appeared within Naruto's subconscious, which surprised both Naruto and the Nine-Tails. As the Nine-Tails stated that Sasuke had similar chakra to Madara Uchiha, Sasuke used his Sharingan to suppress the beast's residual chakra. The Nine-Tails concluded that this was probably its last meeting with Sasuke, so it warned him not to kill Naruto, for he would only end up regretting it. Back in the real world, Sasuke tried to finish off his former team-mates, but he was stopped by Orochimaru and they retreated, leaving Team Yamato to return home.