The discovery of hidden secrets within the Leaf could also prompt Naruto's betrayal in fanfiction. Suppose he finds out that the village has been using dark and unethical means to maintain power, like secretly experimenting on its own people. This revelation could shatter his view of the Leaf as a just and noble place, leading him to abandon it. His sense of justice is very strong, and if the village goes against that, he may not be able to stand by it.
One possibility is a false accusation. If Naruto is wrongly accused of a serious crime like treason or murder within the Leaf village, and no one believes his innocence, he might feel so betrayed that he turns against the village. Another factor could be a conflict of ideals. If the Leaf starts to pursue a path that Naruto believes is morally wrong, such as unjustly attacking another village, he could oppose the Leaf's actions to the point of betrayal.
A plot could involve the Leaf Village betraying Naruto when a powerful and ancient curse is placed on him that makes him seem like a mind - controlled puppet of a great evil. The village, in its panic, decides to take preemptive action against Naruto without fully investigating. This could lead to Naruto having to fight not only the external forces that are trying to use the situation to their advantage but also his own former comrades from the Leaf Village who are now hunting him down.
One possible plotline could be that Naruto is somehow transported to the MLP world. He might be tricked into believing the ponies are a threat and thus 'betray' them by taking actions against them. For example, he could be misled by a dark magic user in that world who convinces him the ponies are hoarding power that could be dangerous.
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 this fanfiction, perhaps Naruto could be under some sort of mind control. Maybe an enemy has found a way to manipulate him into attacking the Leaf. It could also be a case where Naruto is misled about the true nature of the Leaf Village, believing it has committed some great wrong that warrants his attack.
One reason could be to seek more power. In some fanfictions, Naruto might feel that the Leaf doesn't offer enough resources or training for him to reach his full potential. So he decides to leave to find a place where he can grow stronger.
Perhaps Naruto's betrayal in this fanfiction is a result of his own sense of justice that doesn't align with the values of Highschool DxD. He, being godlike, has a different perspective on good and evil. He might view the way the characters in Highschool DxD handle power and relationships as wrong. So, he could start by challenging the most powerful beings in that world, like the leaders of the devil clans or the archangels, which would be considered a betrayal.
It could be because of a power struggle. Suppose Naruto discovers a new, extremely powerful power within himself, but the village elders or some members of Team 7 are afraid of it. They try to suppress him. Feeling cornered and betrayed first, Naruto could then turn against them. He might believe that he has to protect this new power and use it for what he thinks is right, even if it means going against his old team.
The most straightforward resolution could be Hinata explaining the truth to Naruto. Once he knows the real situation behind her 'betrayal', he realizes he was wrong to hate her and they reconcile.
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.
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.