It could be some of the other ninja clans within Konoha. Maybe they envy Naruto's growing power and popularity. They spread false rumors about him or frame him for crimes he didn't commit, causing the rest of the village to turn against him.
The village elders are likely candidates. They are often shown to be power - hungry and manipulative in the Naruto series. They might see Naruto's power as a threat to their control over Konoha and thus plot against him, which could lead to Naruto feeling betrayed.
It could be Sasuke. If he were to turn to the dark side in the fanfiction, his Rinnegan powers could be used to destroy Konoha. He has the potential to be extremely powerful and if he has some sort of vendetta or is influenced by some dark force, he might take his anger out on the village.
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 an evil version of Sasuke. Maybe he has fallen completely to the dark side and manipulates Naruto into destroying Konoha. Or it could be Orochimaru who has found a new way to control Naruto's actions from the shadows.
One possible motive could be a misunderstanding. Maybe Naruto discovers some false information that makes him believe Konoha has betrayed him. For example, if he's wrongly led to think that the village elders are planning to harm his friends or his sensei. Another motive could be the influence of a powerful and evil entity that has somehow managed to control Naruto's mind. It could use Naruto's strength to achieve its own goal of destroying Konoha.
Maybe some of the more conservative village elders. They have always been a bit wary of Naruto because of the Nine - Tails inside him. So they might be behind his capture in the fanfiction.
In this kind of fanfiction, Naruto might be banished due to some false accusations or political conspiracies in Konoha. Once banished, he could decide to destroy Konoha out of anger and a sense of betrayal. He may have learned powerful jutsus during his exile and use them against the village that once rejected 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.
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.
One possible reason could be fear. Naruto is extremely powerful, and some in Konoha might fear that he could one day lose control of his power. Another reason could be political intrigue. There may be certain factions within Konoha that see Naruto as a threat to their power and influence. Also, jealousy might play a part. Naruto has achieved so much and has the love of many, and some might be jealous and thus plot against him.
It could be one of Naruto's former teammates from a mission. Maybe this teammate has some hidden motives or has been bribed by an enemy. They could spread false information about Naruto within the community, making it seem as if Naruto has betrayed them all during a crucial mission. This would cause the rest of the community to lose trust in Naruto.