Kabuto's earliest childhood memory is being found by Nonō on the outskirts of a destroyed village. Suffering from a head wound and amnesia, he had no recollection of his parents or his own identity. The nun treated his wounds with medical ninjutsu and brought him to the orphanage. Shy and reserved, Kabuto did not speak to anyone or thank the nun for her kindness, which led a fellow orphan, Urushi, to question whether or not he had any manners, before slamming a helmet on Kabuto's head to protect his healing wound. When Urushi declared that his lack of a name was annoying, the nun decided to name him "Kabuto", after the helmet. Later that night, Kabuto felt guilty about not thanking the nun and got out of bed to find her, only to get in trouble with the other wards for being up past his curfew. When they took him to a clock to teach him the curfew time, it at first seemed that he was too young to tell time, but the nun recognised that he was squinting and lent him her glasses, allowing him to impress the other caretakers by correctly determining the time of the curfew despite his young age. Because the orphanage could not afford glasses for him, the woman let him keep hers, and Kabuto broke down in tears, repeatedly thanking her as she comforted him.
Prior to the first phase of the Chūnin Exams, Kabuto befriended the members of the Rookie Nine with information on their fellow competitors. During the second phase of the exam, Kabuto joined forces with Team 7 in an attempt to finish the phase with little hassle. When the group encountered Team Oboro, Kabuto's glasses were knocked off of his face after saving Naruto Uzumaki from an attack. This caused Kabuto to momentarily lose his cool and reveal his Killing Intent, paralysing both Team Oboro and Naruto's team-mates as he took advantage to defeat the Ame genin. Upon completing the second test, Kabuto reunited with his team-mates and fellow agents, Yoroi Akadō and Misumi Tsurugi. Back with his team, Kabuto reported to Orochimaru what he had learned about Sasuke Uchiha.
With Orochimaru now in a position to observe Sasuke firsthand, Kabuto forfeited prior to the preliminary matches of the Chūnin Exams. While explaining to Naruto that he was fatigued, injured, and unwilling to risk his life further, Kabuto actually forfeited due to his fear that prolonged fighting would cause him to show his true abilities, blowing his cover. After Orochimaru gathered enough of his own intelligence about Sasuke, he instructed Kabuto to kidnap Sasuke. He was able to take out the eight ANBU members guarding Sasuke and almost succeeded in accomplishing this task, but Kakashi Hatake intervened before he could finish, forcing Kabuto to flee.
Later, he spoke with Baki and they discussed the upcoming Suna and Oto invasion of Konoha. While discussing the upcoming invasion, they realised that they were being overheard by Hayate Gekkō. Kabuto offered to eliminate Hayate, but Baki did so himself. In the anime, impressed by Hayate's skills, Kabuto obtained a hair sample of the Konoha-nin after he fell against Baki, convinced that the sample would prove useful in the future.
During the final matches of the Chūnin Exam, Kabuto kills an ANBU member and poses as him to mingle with the audience. During Naruto and Neji Hyūga's battle, he heals Hinata.
When Sasuke injures Gaara, Kabuto uses a genjutsu to put the audience to sleep and signal the start of the invasion of Konoha. During the invasion, Kabuto has Oto ninja go after Naruto when he starts to pursue Sasuke, fearing what he will eventually become a problem if he is not dealt with soon. However, it appears he already knew it would fail as he wanted to test Naruto. He does not contribute in the battle, pointing out that Kakashi would only copy his abilities, and flees from the village when the invasion fails.
With Orochimaru being heavily injured as a result of the failed invasion, Kabuto accompanies him in searching for Tsunade in the the hope that she can heal his master. Upon finding and in time seeming to persuade Tsunade, Kabuto notices that Tsunade's medical techniques are filled with killing intent, realising her true intentions and stopping her from killing Orochimaru. Knowing that Tsunade will not help willingly, Kabuto resolves to make her help with force. After taking a Military Rations Pill to boost his abilities, Kabuto is able to keep up with Tsunade and land a number of disabling attacks, though she eventually lands a crippling attack upon him. Realising that he is still completely outmatched by the Sannin member, Kabuto manages to turn the fight to his advantage by bleeding himself with a kunai to the hand and uses Tsunade's haemophobia against her.
When reinforcements for Tsunade arrive, Kabuto quickly defeats Shizune before Naruto arrives and surprised that Kabuto is a spy for Orochimaru. While he didn't view Naruto as much of a threat, warning him not to interfere and mocking his dream when beating the younger ninja to an inch of his life, Kabuto finds himself inflicted with injuries he can not fully heal from hit by Naruto's Rasengan. While Kabuto had managed to strike a fatal blow to Naruto's heart before the Rasengan hit him, Tsunade heals Naruto before he can die, leaving Kabuto to lie on the ground, defeated. He later recovers to the point of helping Orochimaru summon Manda, and flees with his master once Orochimaru is defeated.
As Orochimaru anxiously awaits Sasuke's arrival at their lair, Kabuto encourages him to transfer into a new body while he still can, even offering himself. Although Orochimaru rejects the offer, Kabuto finds a strong body for Orochimaru to switch to just in case. In time, due to the Sound Four being hindered by the Konoha ninja sent after them and Sasuke, Orochimaru finally grows tired of waiting and switches to the vessel. While discussing the Sound Four, Kabuto notes Sakon to be the strongest. Kabuto prepared. Kabuto also manipulated Kimimaro to leave to retrieve Sasuke, despite the latter's terminal illness.
When Team Yamato comes to meet one of Sasori's agents, Kabuto is revealed to be that agent. Yamato, disguised as Sasori, is able to learn some things from Kabuto, though just as he is about to capture the latter Orochimaru shows up. Although it seems as though Orochimaru is about to kill Kabuto as a traitor, Kabuto cuts off the Sasori disguise's head, having intended to kill the actual Sasori under Orochimaru's orders. With his cover blown, Yamato calls to the rest of his team for assistance, and Naruto eventually starts to fight Orochimaru. At the start of the battle, Kabuto tries to attack Naruto who has slipped into his three-tailed form, though he is almost instantly repelled a good distance by one of Naruto's roars, knocking out Sakura in the process. He returns back to the bridge and heals Sakura, who had been attacked by Naruto, and hints that the Akatsuki is the greater enemy.
After the battle, Kabuto joins Orochimaru and Team Yamato member Sai in returning to their hideout, and Kabuto is tasked with leaving behind a dead body that looks like Sai to prevent anyone from following them. When Sai is later captured, Kabuto comes to his aid, only to be captured by Sai instead. Unable to escape, Kabuto is forthcoming with information, and discourages Naruto from trying to retrieve the traitorous Sasuke. Kabuto is left by himself as Team 7 searches the lair, though is at some point freed and joins Orochimaru and Sasuke when they depart.
Realising that the time was fast approaching for him to change bodies, Orochimaru sent Kabuto to fetch Guren. When Kabuto nears her location Guren attacks him to see if he is worthy of being Orochimaru's attendant. Satisfied, she accompanies him to Orochimaru's lair and is left in charge of testing the prisoners there and forming a team.
When Guren and her team fail to kill a group of Konoha ninja, Kabuto has them help in summoning the Three-Tails. Kabuto ordered Guren to restrain it with her Crystal Release. When she proves unable to do so, Kabuto retreats upon realising he needs to rethink their strategy.
Later, he begins preparations for a final attempt to capture the Three-Tails during which he secretly meets with Rinji, who is revealed to be a spy for Kabuto. After learning that Konoha has begun attempting to seal away the Three-Tails, Kabuto retrieves Guren and Yūkimaru to stop them.
While successfully stopping the Konoha shinobi from sealing the Three-Tails, they manage to obtain Yūkimaru, much to Kabuto's dismay. Deciding to take desperate measures, Kabuto tricked Kigiri, Kihō, and Nurari into thinking they were dying from the injuries they sustained from the Konoha-nin and convinced them to go through a gruelling operation of having cursed seals forcibly activated.
He then disguises himself as Rinji, tricks Yūkimaru to use his power to unleash the Three-Tails' full might despite knowing how weakened Yūkimaru was. After a failed attempt to have Yūkimaru make the Three-Tails go on a rampage, Kabuto, disguised as Rinji, reveals to Yūkimaru that it was Guren who killed his mother, but is shocked that Yūkimaru forgives her. He then attacks Guren and Yūkimaru with scalpels, but are deflected by Naruto. Naruto throws one of the scalpels cuts Rinji's face which turns out to be a mask and it falls off, revealing that he is Kabuto.
Since his meeting with Rinji, Kabuto has been posing as him. Kabuto and Naruto fight it out, with Naruto having improved enough to seemingly gain the upper hand over Kabuto. As Guren tries to escape with Yūkimaru, Kabuto then summons Rinji with his Dead Soul Technique to stop her. Guren fights him, only to be immobilised by his bats. Guren who made her promise to protect Yūkimaru at the cost of her life grabs Rinji from behind and sacrifice herself to kill him. Yūkimaru then screams in agony at what appears to be the loss of Guren. The screaming once again awakens Yūkimaru powers and causes the Three-Tails to breaks out of the seal and go on a rampage. Kabuto then leaves the scene satisfied with what was happening.