Academy Entrance Arc
Mitsuki transferred to Konoha village to start his new journey, after Naruto Uzumaki, who is the Seventh Hokage of the Konoha village, accepted Orochimaru’s request to let Mitsuki have a normal life like the other kids.
Mitsuki joined the Ninja academy, and since he arrived in Konoha, he has kept his eye on Boruto Uzumaki, because he wants to know if Boruto would show him the right path for him to follow. He met Boruto for the first time when Mitsuki caught an expelled academy student who was damaging the village property, after Nue possessed him and made him do so.
On the following day, Mitsuki was introduced by Shino Aburame in his class, where he sat with Boruto. From the start, he wants to help Boruto in every manner, like he did when Boruto could not solve an equation that Shino gave. Later, when Iwabee Yuino wins a match against Boruto in combat training, Mitsuki fights Iwabee and is about to hurt him before Shino and Boruto stop him. At night, he reported about his day to Orochimaru.
The next day, Shino hosted a welcome party for Mitsuki. During the party, some of the students were alarmed by Shino's bugs, so Mitsuki agreed with Denki Kaminarimon's request to get rid of the bugs and used Wind Release to blow them away. His actions result in the destruction of the party location.
Then, as Boruto and the other students were fighting with a possessed repairman who was on the rampage, Mitsuki arrived to save him. The incident made Shino feel bad that his absence had put the kids at risk, and Nue took advantage of his sorrow to control him. Shino scheduled Mitsuki, Shikadai Nara, and Boruto to meet him for after-school sessions outside the village the following morning. When he stated that he would kill the troublemakers, the three were forced to run into the woods, where Mitsuki suggested their only option was to kill their teacher. Later, they were able to free their teacher from possession. Soon, the Nue incident was solved by Mitsuki, Boruto, and other Konoha shinobi.
Shino made the decision to switch up the three-man teams for their next challenge a few weeks after Sumire and Nue's incident was solved. Mitsuki teamed up with Metal Lee and insisted on staying on Boruto's team. They were relieved to see Sumire back in their class as they started talking about rumors that she was being transferred to a different school.
School Trip Arc
Shino's class visited Kirigakure on a field trip, and Kagura Karatachi led them into the village. Their journey took them to well-known tourist destinations, where they met the Fifth and Sixth Mizukage. The class then watched as Boruto got into a fight with Kagura Karatachi in the Kirigakure Academy. Mitsuki assisted his classmates in rescuing Denki Kaminarimon when he was taken hostage by a group of juveniles who respected the "Bloody Mist Village" period. When the students faced Tsurushi Hachiya's gang, they were able to save Denki and take down the rookie shinobi. The kids and Kagura played Shinobi Bout at their hotel following the incident.
The following day, Suigetsu escaped as Mitsuki approached him near the Seven Ninja Swordsmen of the Mist weapon vault. Suigetsu later came up to Mitsuki in an alley and told him that Orochimaru didn't want him to take part in the coup that Shizuma Hoshigaki was planning. Suigetsu hated Shizuma's group, and Mitsuki received a scroll from him that revealed details about officials from the Land of Water administration holding covert talks with the Land of Waves. Mitsuki watched Boruto and Kagura defeat Shizuma and end the coup before it began.
Graduation Exams Arc
Before the graduation exam, every student was asked to bring their parents with them and also think about what their future plans are in life. Mitsuki's father, Orochimaru, also attended the meeting secretly and asked Mitsuki about his plans. In reply, Mitsuki wished to be in Konohagakure with Boruto, which Orochimaru accepted.
In the graduation exam, Mitsuki passed the written test alongside everyone as well as the 2nd exam, which was against the Ninja Academy teachers and Kakashi Hatake. Kakashi gave them the task of getting the bell, which they failed to do, but in the end, Kakashi passed them in terms of their team coordination and their will to win together. After they became Genin, Mitsuki was placed in Boruto and Sarada's team, first called Team 3, later changed to Team 7.
Genin Mission Arc
Team 7's first Mission, which required protecting Green Banks from robbers, was given by Naruto to them. When the team discovered that the bandits were actually ninjas upon arrival, Konohamaru questioned whether they should continue with the assignment because it would likely be too challenging for Genin to take on skilled shinobi.
The genin saw Ashimaru attack the village while he was speaking with Kiri about the situation, which forced Konohamaru to force Ashimaru to retreat. In order to force her into giving them the title to the village's bridge, Kiri explained that the shinobi were attacking the village. Team 7 discovered that several villagers were under the genjutsu control during the night and took them down.
Team 7 met with the culprits after learning that Kiri had been kidnapped during the event to trade the deed for her. After the exchange, Hidari and Ashimaru decide to kill everyone, which prompts Konohamaru to ask the genin to accompany Kiri in her escape. Attacked by Ashimaru, the missing-nin was confronted by the genin, who used Boruto Stream on Sarada to defeat him. The team finished the mission and went back to Konoha.
Byakuya Gang Arc
The team discovered the Byakuga Gang had looted the Konoha Bank after completing their mission, which included apprehending an attacker there. The genin went to Katasuke for help when Sarada decided it was done utilizing Ice Release. He disclosed that the thief intended to sell the stolen things, and the three genin devised a scheme to thwart the sale and apprehend the culprit.
They try to catch the thief as they approach him, but he manages to escape and run towards a town, leading them to follow. The burglar revealed that he had already sold the stolen gems to pay for the town's water wheel repair there, justifying his conduct. Sarada and Mitsuki started to pursue him as he ran, but they gave up when Boruto seemed ambivalent about the situation.
Versus Momoshiki Arc
Mitsuki entered the Chunin exam with his teammates. The first stage was to guess the right answer, but the surprise was that both answers were wrong and all the students fell into ink, but Mitsuki and Sarada somehow saved Boruto and themselves and were able to pass the first stage. In the second stage, they had to capture the opposite team’s flag while defending theirs. Boruto used the Ninja tool secretly and was able to win the 2nd stage. In the third stage, they had to fight one-to-one against their opponents.
Mitsuki defeated Toroi in the third round. Later, after Boruto was disqualified, Kinshiki and Momoshiki began their attack. Children are helped to leave the area by Mitsuki and Sarada. He was relieved when he saw that Sarada had been saved by her father after initially being worried when it appeared that she had been crushed by falling debris.
In order to help Boruto, Mitsuki activated Sage Mode, but before he could, he was attacked by Urashiki Otsutsuki, who took some of Mitsuki's chakra and knocked him out. During this time, Naruto protected Mitsuki from Momoshiki's final strike on the location. Mitsuki, Sarada, and Sakura Uchiha watched Boruto depart the village with the four Kage to rescue Naruto after he had been captured alive by Momoshiki Otsutsuki and Kinshiki Otsutsuki.
A few days later, Mitsuki saw Orochimaru in secret. Orochimaru cautioned him against using his Sage power in front of people, but Mitsuki disregarded him because he believed it was vital to aid Boruto, who had grown to be his shining star. Orochimaru agreed to this and departed, asking Mitsuki to visit the house occasionally so he could observe his son's development.
Chocho Arc
In order to take part in an upcoming mission, Mitsuki brought Orochimaru a scroll to sign. But before he signed it, he did some sparring with Mitsuki to test his development. He praised Mitsuki's development even though Orochimaru easily defeated him.
When Mitsuki questioned whether he should refer to Orochimaru as his father or mother, the man said that it didn't matter because he had been many different things throughout the years and that what matters most is one's heart.
The Kage Summit was held in Konoha, and Team 7 was tasked with providing security. Mitsuki started thinking back on his first dream, a memory from when he initially decided to follow his own interests. As a result, Mitsuki started to consider how one could tell if their will was actually their own or just an attempt to control others. Changing the subject, Boruto told his teammates about a recent puzzle Naruto posed to him regarding the existence of the hardest stone. They observed that a search party was looking for Onoki, who had wandered off as they tried to come up with the solution. After the meeting, Onoki told Mitsuki that his will was not steady and he started to question himself.
Mitsuki's Disappearance Arc
When Mitsuki went home after their mission was finished, he found a letter from a bunch of Iwagakure shinobi, which led him to burn it. The following morning, he left the village's boundaries and met with Sekiei, Kokuyo, and Kirara to see if he could get Ku, the group's leader, to teach him the secret of one's will.
When Sao and Uo learned about their meeting, the group attacked them. Before the Iwagakure shinobi could kill them, Mitsuki used his snake to stop their heartbeat temporarily and then left Konoha village with them. Soon, they were followed by Konoha shinobi, who were engaged by Kokuyo and Akuta.
When Sekiei found out that two shinobi had gotten past Kokuyo, he had two Akuta guard him while he went to fight the Konoha shinobi, who were Sarada and Boruto. Mitsuki followed Sekiei, saved Sekiei, and attacked Boruto, surprising Sarada and Boruto himself.
Later, as Sekiei's body began to crumble again, Kokuyo left Mitsuki to watch after Sekiei while he searched for assistance. Sekiei suddenly caught Mitsuki in one of his clay insects while they were alone together, revealing that he knew Mitsuki had saved Uo. The two accepted that Mitsuki had no hidden objective other than discovering who he truly was, and when Kokuyo's comrades joined them, Sekiei was moved to testify to Mitsuki's trustworthiness.
When Mitsuki arrived at Ku's headquarters, he was shown around the place, including his own space and Sekiei's, where he had drawn many of the individuals he cared about. A scientist was brought in to examine Mitsuki's special body. A Cursed Seal was discovered to be implanted in his heart after testing. Later, when he finally met Ku, he questioned the nature of free will. Ku said that Mitsuki is an artificial human. Therefore, he can't really answer that question, and the only one who can is Orochimaru, his creator.
He did point out that Mitsuki's betrayal of Konohagakure was an act of rebellion, which is common among humans as a sign of maturity. He continued to claim that the Third Tsuchikage's plans to establish long-lasting peace through the Akuta would succeed only if the special qualities of Mitsuki's being were fully utilized. Later, Mitsuki discovered that a masked Konohamaru had located and entered the base. Mitsuki was given a chance to explain when Konohamaru showed himself.
Mitsuki apologized for the trouble he had caused everyone and promised to take responsibility for his actions, but he insisted he must end it the way he thought was right. Reminding him that he would always be a part of Team 7, Konohamaru made the decision to have faith in him. Soon after, Mitsuki brought Ku a heart for a transplant. When Sarada and Boruto arrived, Mitsuki launched an attack to stop them. Mitsuki then attacked Ku from behind and disclosed that snakes hid within the heart. Boruto's promise that he would pay attention to what he had to say when they got home gave Mitsuki comfort. After defeating Ku and other artificial humans, they returned to Konoha.
Konohamaru and Sai detained Mitsuki after he got home so they could question him about his recent actions. It was ultimately determined to forgive Mitsuki because his actions weren't dangerous and they instead benefited Iwagakure. He was nonetheless punished by having his shinobi rank taken away. Mitsuki apologized for his recent behavior and acknowledged his selfish desire to interact with others who were more like himself. To Mitsuki's surprise, Boruto quickly accepted his apologies and acknowledged that he was happy that he had the opportunity to get to know Mitsuki better as a person. Later, the decision was made to restore Team 7 genin's shinobi status due to Kurotsuchi's appreciation and recommendation.
Later, Mitsuki played an important role in many missions. Firstly, in the Jugo arc, he saved Konohamaru from the scientist. Alongside Boruto and Sarada, he was able to help Jugo, and they were successful in helping the birds and fish around that area. In the Time Slip Arc, he was in the genin squad that fought against Urashiki Otsutsuki. In the Mujina Bandits Arc, Mitsuki, Boruto, and Sarada went undercover at Hozuki castle, solved the case, saved Kakuri from the gang, and returned to Konoha with Kakuri so Kakuri could give them intel about the Mujina Bandits. They were able to capture all the members of the Mujina Bandits.
In the Kara Actuation Arc, Mitsuki saved Boruto and Sarada from Deepa by using Sage mode and risking his life. Later, they were able to defeat Deepa, and Orochimaru destroyed the God Tree. In Ao's arc, He, with his teammates, is able to defeat Ao, who was with the Kara group.
Mitsuki saved Kawaki, Boruto, and Sarada against the virus which was used by Boro when he captured Naruto, and in the rescue of Naruto, he played an important role in saving all his comrades and Naruto. In the Great Sea Battle of Kirigakure Arc, Kawaki joined Team 7 officially as genin and successfully completed their mission.