The Biggest Mistake Naruto's Kabuto Ever Made That Turned Him Evil
Naruto author Masashi Kishimoto has a habit of making many of his major antagonists sympathetic. Even the series' most ruthless villains are known to have sad backstories that either motivate their current evil actions or provide Naruto an opportunity to convert said villain to the side of good. Villains like Zabuza Momochi, Obito Uchiha, and Gaara are all examples of antagonists whose histories add emotional depth and conflict to their characters.
Like Gaara, many of these characters eventually find themselves turning a new leaf once they realize being evil isn't really the best way to deal with their emotional baggage. Such was the case for Kabuto Yakushi, who faithfully served a number of antagonists as a spy and medical ninja throughout the series before going solo with his morally rotten escapades. Kabuto would eventually find redemption by the end of Naruto's final arc but not before doing some seriously heinous stuff first.
What did Kabuto do that was so evil?
Like most Naruto villains, Kabuto wasn't born bad. According to Narutopedia, he started out as a normal child from the Land of Fire. However, one day, his village was destroyed, and the very young Kabuto was injured, giving him full-blown amnesia. However, the toddler is soon found and brought to the Leaf Village's orphanage, where he would've had a happy upbringing were it not for Danzo, leader of the Root division of the village's Anbu Black Ops.
Danzo was looking for Root recruits and managed to enlist both Kabuto and his caretaker, Nono, into the organization. Kabuto performed many acts of espionage for Root but left the organization after being manipulated into killing Nono, whom he saw as a mother. After that, Kabuto enlisted under the command of one of the Leaf Village's deadliest enemies, the evil Sannin Orochimaru.
While it makes sense that Kabuto would join Orochimaru to defy the village that manipulated him, he does some pretty nasty deeds on Orochimaru's behalf that seem incompatible with his backstory. For example, he medically experiments on live children. You'd think after being manipulated as a child that Kabuto would be more protective of kids in the ninja world. Unfortunately, that's not the case. And though Kabuto eventually redeems himself and takes over as the head of his old orphanage, his ruthless experiments are hard to forget.