The Hokage at the time, if it's someone like Kakashi or Tsunade. They have a great deal of experience and power. They could try to reason with Naruto first. If that doesn't work, they'd use their strongest jutsus to try and subdue him. For example, Kakashi could use his Lightning Blade or Tsunade could use her super - strength punches.
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.
Maybe the combined efforts of all the jonin in the Leaf Village could stop Naruto. They could form a united front and use their different skills and jutsus. Some could use genjutsu to try and trap Naruto in an illusion, while others use ninjutsu to attack him. They'd have to be very careful though, because Naruto is extremely powerful.
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.
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.
The combined forces of the remaining ninja clans in Konoha could also pose a threat to evil Naruto. If they put aside their differences and work together, they could pool their resources, jutsu, and manpower to try and halt Naruto's rampage. Although Naruto is extremely powerful, the collective strength of the village's ninja clans could potentially be enough to subdue him.
The hidden enemies within Konoha who oppose Naruto's ideas of peace and unity could be antagonists. They might spread false rumors about Naruto, turning the villagers against him. This growing animosity between Naruto and the village could result in him lashing out at Konoha, making those who spread the rumors antagonists in the fanfic.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.
It could be a new character that we haven't seen in the original Naruto series. This character might be jealous of Naruto's power and wants to see him destroy his own world so that he can take over the chaos that follows.
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.
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.
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.