Maybe Naruto is framed by a powerful enemy within Konoha. False accusations are made against him, and instead of getting a fair trial, he is hunted down. This injustice could make him turn his back on the village that he once loved and swore to protect.
It could also be due to a conflict in ideology. Suppose there is a new leadership in Konoha that wants to take a more aggressive and unethical approach towards other villages. Naruto, who has always believed in peace and understanding, might oppose this so strongly that it results in him being seen as a traitor to Konoha.
One way could be through a misunderstanding. Maybe they believe Hermione has done something wrong, like they misinterpret her actions regarding a dangerous spell she was researching. So they distance themselves from her, which she sees as a betrayal.
Well, in a fanfiction context, it could be possible if we consider a crossover universe where Naruto somehow ends up in the Star Wars galaxy. Maybe he's brainwashed by the dark side's influence which is similar to some dark forces in his own world. This could lead him to betray the Jedi ideals that he might have adopted during his time there.
In some fanfiction, Naruto might be depicted as destroying Konoha due to extreme circumstances. Maybe he was pushed too far by the village's mistreatment or a misunderstanding. For example, if the village turned against him despite all his efforts to protect it, his pent - up anger and power could lead to such a drastic outcome.
In a Naruto kills Kiba fanfiction, one way it could be developed is through a misunderstanding. Maybe Kiba is framed for a crime against the village that Naruto believes wholeheartedly. Naruto, in his overzealous sense of justice, might attack Kiba without fully understanding the situation. However, this goes against Naruto's character in the original series, so it would require a significant deviation from the canon.
One way it could be developed is through extreme despair. Maybe Naruto fails to protect the village from a new and overwhelming threat. He blames himself so much that he starts to think his death would be a solution. For example, if all his friends were killed in the battle and he felt powerless to stop it, he might sink into deep depression and consider suicide as a way to end his pain.
Perhaps Fem Sasuke is brainwashed by an enemy. This enemy could use some sort of mind - control jutsu on her. They plant false memories or ideas in her head, making her believe that Naruto has become a danger. She then betrays him, but as the story progresses, she starts to break free from the mind control and realizes her mistake.
Well, one way it could develop is that Percy is somehow influenced by an outside force, like a powerful enemy who has control over his mind. Maybe this enemy makes Percy believe that Artemis is a threat to his friends or the world. So, Percy, in his clouded state, starts to act against Artemis, leading to a series of events where their relationship deteriorates. This could involve Percy leaking Artemis' secrets or undermining her plans.
Well, one way could be that Padme is from a different ninja village and is on a secret mission. She gets close to Naruto to gain information about Konoha. When she gets what she needs, she betrays him by revealing his secrets or setting him up in a dangerous situation. For example, she could tell his enemies his fighting patterns or the location of his important allies.
In some fanfictions, there could be an alternate reality or a time - travel plot involved. Maybe Kakashi from the future accidentally goes back in time and in the chaos of trying to fix something, he ends up killing Naruto. This would completely change the course of the Naruto - verse. Characters like Hinata, who had feelings for Naruto, would be heartbroken. And the Akatsuki might take advantage of the situation, seeing the Hidden Leaf Village in a state of disarray without Naruto as their potential Jinchuriki and future hope.
One way this could be developed is if Naruto is somehow mind - controlled. For example, an enemy uses a powerful genjutsu on Naruto, making him lose his sense of self and see the Third Hokage as a threat to the village instead of a protector. Then, in his confused state, he attacks and kills the Third Hokage. This would create a huge moral and emotional conflict within the story, not only for Naruto when he comes to his senses but also for the entire village.