Jealousy could be a reason. Suppose Neji has achieved something that Naruto desperately wants, like a high - ranking position in the village or a special recognition. Naruto's envy could turn into anger and fuel a fight where he overpowers Neji. Another reason could be a misunderstanding. Maybe Neji is wrongly accused of something that Naruto holds dear, like endangering a friend. Naruto, in his haste to protect and seek justice, attacks Neji with full force.
One possible plotline could be that Naruto has a sudden and extreme power-up that makes him overconfident. This overconfidence leads him to challenge Neji in a spar that gets out of hand and he ends up 'destroying' Neji in the sense of completely overpowering him. Maybe Naruto has unlocked a new form of his chakra that Neji can't counter with his Gentle Fist technique.
Well, it could be due to a plot twist in the fanfiction. The author might want to show Naruto's growth in a more extreme way. Naruto could have received some special training from an unknown source that gives him an edge over Neji. He might also be under the influence of a special power - up item or a curse that enhances his abilities but also makes him more violent. In that case, his strength could easily overpower Neji's skills.
Yes, there might be such fanfics out there. In the Naruto fandom, with a large number of fans creating various types of stories, it's possible that some would write a story where Naruto destroys Sasuke in a way that could be seen as Sasuke - bashing. However, these kinds of fanfics may not be in line with the overall spirit of the original work which focuses on their complex relationship and growth.
There's a fanfic called 'Neji's Redemption'. In this, it focuses on Neji's journey after certain events in the Naruto series. Naruto plays a crucial role in helping Neji find his true path. It's a very character - driven story that fans of their dynamic will enjoy.
Sasuke might be able to stop Naruto. They have a long - standing relationship and Sasuke has always been Naruto's equal in terms of power. He could use his Sharingan to try and break whatever is controlling Naruto or just fight him head - on and appeal to their old friendship.
It could be an organization similar to the Akatsuki, but with a different goal. Instead of collecting tailed beasts, they are focused on conquering villages. Their army would be made up of powerful and diverse fighters, and Naruto would have to face their leader, who has some sort of special power or ability that makes them a formidable foe.
The theme of justice might be present as well. If 'kina' is something evil or causing harm in the fanfic, Naruto's destruction of it can be seen as an act of justice. Also, the fanfic could explore the theme of sacrifice. Naruto might have to sacrifice something, like his time, energy or even relationships to be able to destroy 'kina' successfully.
It could be that Naruto is possessed by an evil spirit. This spirit wants to destroy the Leaf Village for its own reasons. Naruto, under its control, would first cut off the village's supply lines, making it difficult for the villagers to get food and resources. Then, he'd start attacking the ninja in the village one by one. He might even use his Nine - Tails chakra in a very destructive way, not caring about the harm it would cause to the place he once called home.