Sai was assigned to join Team Kakashi by his superior Danzō to assist in meeting with a spy in Orochimaru's ranks to find out about Sasuke Uchiha. Sai is confrontational with his new team-mates, questioning Naruto's manhood and insulting Sasuke. The latter causes Sakura Haruno to punch him in anger. As they continue on to the meeting point, Sai questions why Naruto is loyal to a traitor like Sasuke, to which Naruto said he's not a traitor, but a friend.
Upon reaching the designated meeting place, Yamato went ahead disguised as Sasori so that he could meet the spy. When the spy, Kabuto Yakushi, arrived with Orochimaru to kill Sasori, Sai, Naruto, and Sakura were called in for help. When Naruto and Orochimaru begin fighting, Sai leaves the rest of the team to begin his real mission. He observed Naruto's fight with Orochimaru, unconcerned with the danger he left Yamato and Sakura in, and approaches Orochimaru after he had repelled Naruto with a proposition from Danzō. Orochimaru accepted, and Sai accompanied him and Kabuto back to their hideout.
Once arriving at Orochimaru's hideout, Sai was introduced to Sasuke, who had been training under Orochimaru for the past two-and-a-half years. When Sai mentioned that he might get along better with Sasuke than he did with Naruto, Sasuke fixed him with a stare, startling Sai due to the amount of fear it gave to his emotionless self. He was led to his own room afterwards by Kabuto, who locked Sai in upon leaving. Soon afterwards, Team Kakashi tracked Sai down and confronted him about his real mission. Caught, Sai explained that he had been assigned to ally with Orochimaru on Danzō's behalf so that the two may join forces in destroying Konohagakure.
Disgusted by the ramifications of this plan, Team Kakashi restrained Sai before setting out to find and retrieve Sasuke. Sai, however, doubted their success, stating that Sasuke no longer cared about them. Naruto, in response, stated that he used to hate Sasuke, but over time he had formed a bond with Sasuke through their shared experiences, and as such he would do whatever it took to bring Sasuke home. Naruto's dedication to retrieving Sasuke struck a chord with Sai, who was left without words as a result. When Kabuto arrived and freed Sai, Sai instead helped to capture Kabuto, hoping to accompany Naruto to find out more about bonds.
Naruto and Sai split away from Sakura and Yamato to go looking for Sasuke. They are soon found by Orochimaru, and Naruto distracts him so that Sai can have a chance to scout on ahead. When Orochimaru retreats and Naruto reunites with Sakura and Yamato, Yamato goes through the belongings that Sai left behind. In doing so he discovers Sai's actual mission: to kill Sasuke as a traitor to Konoha. Team Kakashi races through the base to find and stop Sai, but Sai has already found Sasuke. Sai, however, truly had a change of heart, and tries to capture Sasuke in order to protect his bond with Naruto.
Irritated by Sai's reasons for bothering him, Sasuke attacks Sai, drawing the rest of the team to their location. When they find out what Sai was trying to do, they all team up to restrain Sasuke. Although Sai is able to land a successful attack, Sasuke's abilities are too much for them and he prepares to kill them all. He is stopped by Orochimaru and Kabuto, who convince him to spare the team before leaving. Defeated, Team Kakashi returns home. Sai requests that he be allowed to stay a part of the team and, with Danzō's approval, begins spending time with his new friends.
At one point, Sai begins visiting the Konoha library to read about relationships in the hopes of making some for himself. In the anime, this begins before and continues throughout the Twelve Guardian Ninja Arc. When he reads that nicknames are a good way to make friends, Sai makes the mistake of using nicknames that describe how he actually sees a person. When calling Sakura "ugly" earns him a beating, he concludes that women like to be called the opposite of what is true. To that end, he calls Ino Yamanaka "beautiful", something that receives another beating from Sakura.
Sai and the rest of the team are later sent to provide backup for Team 10 during their battle with Akatsuki. Because Shikamaru Nara was separated from the rest of the group, Sai and Sakura were sent as backup for him, though upon arrival they found that Shikamaru had already defeated his opponent. Sai returned with everyone else to Konoha, having not taken part in the battle. Because Naruto was injured during the battle he has difficulty eating when they get back. Sai, to improve their friendship, feeds Naruto, angering Naruto because he had wanted Sakura to feed him. Neither has their way when Kakashi arrives to feed Naruto instead.
Along with Team Kurenai, Sai and the rest of Team Kakashi set out to find and capture Itachi Uchiha. When Kakashi summoned his ninken to assist them on the mission, Sai is partnered with Ūhei and Urushi and wonders to himself whether or not he could become friends with dogs. He and the others are later confronted by Tobi, who stalled them long enough to prevent them from locating neither Sasuke nor Itachi.
When Naruto entered the Hokage's office, he is seen with Sakura, the toads, Shizune and the Hokage when Naruto learnt of his master's demise. During the invasion of Pain, Sai is away with Yamato and Anko Mitarashi, tracking down Kabuto Yakushi. He used a special tracking technique that can not be detected by Kabuto. Anko even congratulated him for that. They stopped the search just after a surprised Yamato tells the group that Naruto has reached the six-tailed form of the Nine-Tails.
Five Kage Summit Arc Edit
After the invasion, Danzō is made Hokage. He summons Sai before him and instructs him to keep an eye on Naruto. Sai asks why, so Danzō explains that Naruto, having defeated Pain, is the village's hero and thus more popular than Danzō himself. However, he is still the village's jinchūriki and must be kept in check. Sai is satisfied and goes to meet with Naruto and Sakura. The two immediately confront him about Danzō, asking that he tell them everything he knows. Sai says that he cannot, as the cursed seal Danzō placed on his tongue prevents him from revealing anything about Root. Sakura says it is cruel, but Sai explains that it is for the best since Root has done a number of questionable things to protect the village.
Sakura refutes his claim, pointing out that Danzō has ordered Sasuke be killed as a traitor. Sai is surprised, Danzō not having told him that during their meeting. They are immediately confronted by Kumogakure ninja who after their brief skirmish ask for what they know about Sasuke. Naruto, seeing that this upsets Sakura, volunteers to tell them all that he knows. Sai secretly watches the meeting and how Naruto cannot bring himself to sell out Sasuke.
Naruto allows Karui to take out her anger on him. Karui happily accepts and begins beating him up, but Sai steps in once she starts to overdo it. When Karui leaves, Sai brings Naruto to Kakashi and Yamato and then tends to his wounds. Naruto asks that Kakashi and Yamato help him find the Fourth Raikage. When they agree, Kakashi tells Sai not to tell Danzō what Naruto is doing. After hearing such a request Sai looks rather upset and asks Kakashi if he doesn't trust him because he is from Root, but Kakashi answers that he believes in him because he is also a member of Team Kakashi. Hearing these words makes Sai happy and drives him to act more resolutely. Sai later approaches Sakura, telling her about what Naruto went through with Karui for her benefit. He surmises that Naruto loves Sakura, and that trying to make her happy, such as bringing Sasuke back to the village, causes him constant pain.
Following the Konoha 11's decision to eliminate Sasuke themselves to prevent a war, Sakura asks that Sai help her track down Naruto so that she can speak with him. They find him in the Land of Iron and Sakura tells Naruto that she loves him, so now he doesn't need to bother fulfilling his promise of retrieving Sasuke. When Naruto claims she is lying she leaves. Because she doesn't mention the decision to kill Sasuke and that he feels responsible for what she was about to do because of what he told her back in Konoha, he leaves an ink clone behind to tell them what Sakura did not. The clone also adds that Sakura is likely planning to kill Sasuke personally, and mentions that Sakura is still in love with Sasuke and wants to stop him from sinking any lower.
The ink clone helps Kakashi locate Sakura. The real Sai, meanwhile, stops Sakura from knocking him out and her other escorts, having suspected that she would try to get rid of them so she could fight Sasuke alone. Sakura convinces Kiba and Lee that Sai is a traitor and they start to fight him, but this only makes it easier for her to knock out all three. As the ink clone disperses it warns Kakashi of Sakura's actions. Sai and the others are later woken following the meeting with Sasuke, and as they return to the village they are met by three Root members. They inquire about what has happened. Sai affirms that the seal disappearing is proof that Danzō has died. He then encourages them to speak with Kakashi who he addressed as the "new Hokage" about Root's future.
When the Fourth Shinobi World War begins, Sai is placed in the Surprise Attack Division. He creates birds with his Super Beast Imitating Drawing for his Division to head into battle. When they enter enemy territory and the rest of the division begins making a base camp, Sai takes to the air to provide back up in case they are attacked. When he later sees several explosions near the camp, Sai rushes back, eliminating one enemy as he arrives. Despite having a broken neck, the target gets back up, revealing himself to be a reincarnated Shin. Shin apologises to his brother for being forced to fight him, unable to control his own movements because of the technique he was reincarnated with and because he was also being manipulated by Sasori. Sai and Shin trade blows until the rest of ambush team can come to help. Hoheto Hyūga reveals that there is explosive clay stored within Shin. They navigate him into one of Kankurō's puppets before he can detonate, weakening the explosion.
However, the force is still great enough to knock Sai over and release some of his belongings from his bag. Shin regenerates from the damage and Deidara promises to use Shin as a human bomb again and again. Enraged, Sai quickly navigates behind Deidara and Sasori draws two ink warriors that knocks both into two more of Kankurō's puppet, where they are confined and neutralised. Sai then prepares to fight Shin again, but Shin tells him there is no need; Sai had dropped his picture book earlier, and seeing the finished product had unbound his soul, freeing him of the regrets that he had in life. Tears flow from Sai's eyes as Shin's body turns to ash and dust.
Sai, Omoi, and Zaji are sent out to find other Akatsuki cells. When they come across a group consisting of Haku, Zabuza, Gari, and Pakura, Sai creates several ink birds with explosive tags attached to bombard them with. Although the revived ninja recover from their injuries, Sai continues the assault until backup can arrive. Haku manages to destroy the birds they are riding, causing them to fall to the ground. Before they can be killed the Third Division arrives to help. They later join the division protecting Kakashi while he executed his strategy.
After Zabuza and Haku are dealt with, Kakashi asks that Sai back him up with the sealing techniques he learned from Root. Sai is reluctant, but Kakashi insists that, as one of Danzō's most prized soldiers, Sai doesn't need to hold his emotions. Later, Sai is seen among with the rest of the Third Division as they recuperate after the first day of war.
The next morning, Sai alongside the Third Division restart their assault on the Seven Ninja Swordsmen of the Mist. Drawing a gigantic tiger, Sai launches his Sealing Technique: Tiger Vision Staring Bullet at Fuguki Suikazan who had been incapacitated by Kakashi. As the tiger drags Fuguki back into the drawing, Sai noticeably winded tells them that he can still go on. Lee tells Sai to just concentrate on sealing the enemies, he would protect him. As a new wave of White Zetsu Army clones approach, Sai looks on as Naruto's shadow clone arrives on the battlefield to confront them. In the anime, Sai also used this technique to seal away Jinin Akebino, and a number of other reincarnated shinobi as well.
After being informed by Inoichi from HQ that Naruto and B were fighting the "masked Madara", Sai and the Konoha 11 rush to his aid. As he ran, he stated that if it weren't raining he could use his Super Beast Imitating Drawing technique to get to Naruto faster. After Lee however, spurred him on, he thinks to himself that he finally and completely understood what it meant to have friends. Upon arriving at the battlefield, he apologised to Kakashi for their late arrival and later stood alongside the remaining members of the Allied Shinobi Forces to face their opposition.