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.
One possible reason could be a threat to Konoha. If Iwa planned an attack on Konoha, Naruto, as a defender of his village, might take the fight to them and end up destroying parts of Iwa in the process.
Maybe Naruto is just teasing Neji. In the Naruto world, friends often playfully taunt each other. Naruto might have seen Neji do something that he thought was more like what a girl would do, like being overly cautious or having a particular grace in his movements. It could also be a random joke that Naruto came up with to get a reaction out of Neji.
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.
In the fanfic, Naruto might destroy the army in a very unique way. Instead of using his typical Rasengan or Shadow Clone Jutsu, he could discover a new power within himself. Maybe he unlocks a special form of Sage Mode that gives him the ability to control the elements in a completely different way, allowing him to take on the army with ease.
A possible plot might involve Naruto being exposed to some ancient and powerful knowledge or artifact. This discovery gives him the means to 'destroy' bloodlines in the sense that he can change the very nature of chakra within a person. He might use this new - found ability to break the cycle of bloodline - based power hierarchies. He could start with the major clans like the Uchiha and Hyuga, and as he spreads his influence, the concept of bloodline superiority slowly crumbles, leading to a new era in the Naruto world where a person's worth is determined by their own efforts and skills rather than their bloodline.
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.
Some secret organizations that have been manipulating bloodline abilities for their own gain could also be the antagonists. They would not want Naruto to disrupt their plans. They might send their most powerful agents to stop Naruto, leading to intense battles in the fanfic.
One possible motive could be a dark or alternate universe take. Maybe in this fanfic's world, there is some sort of dark magic or mind control that forces Naruto to do it against his will.