Kaguya Otsutsuki might be the main antagonist too. She could be resurrected and plant false memories or emotions in Naruto, making him think Konoha is the enemy. Or perhaps a character from a different anime or manga crossover into the Naruto world and play the role of the antagonist, pushing Naruto to destroy Konoha.
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.
Madara Uchiha could also be a likely antagonist. Even if he is dead in the original story, in a crossover fanfiction, he could be brought back in some form and use Naruto as a weapon against Konoha. Another possibility is a new, original character created specifically for this fanfiction, a powerful and devious ninja with a vendetta against Konoha who uses Naruto's power.
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.
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.
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.
It could be a corrupt elder in Konoha. They might be power - hungry and see Naruto as a threat to their control. So they manipulate the situation to make Naruto the enemy.
Perhaps in this fanfiction, there is a dark prophecy that Naruto misinterprets as Konoha being the source of all evil in the ninja world. So, in his attempt to 'save' the world, he decides to destroy Konoha. Also, it could be that an evil entity has merged with Naruto, and the combined power has a grudge against Konoha for some past event.
It could be a rogue ninja from within Konoha who has embraced the 'darkness' fully and wants to reshape the village according to his own twisted ideals.
The main antagonist could be a new character. For example, a powerful ninja from a rival village who has a vendetta against Konoha. This ninja could manipulate Naruto into leaving Konoha by spreading false rumors about the village. Then, he tries to use Naruto's power as an assassin for his own evil plans.
It could be a long - lost relative of one of the old villains like Orochimaru. Maybe this person has been in hiding, training and growing in power, and now wants to take revenge on Konoha for what happened to their family member.
Maybe the main antagonist is a powerful figure within Konoha who doesn't want Naruto to leave and become an independent force. He secretly sends assassins after Naruto. When Temari gets involved, this figure also targets her. His actions are driven by his thirst for power and fear of Naruto's potential outside of Konoha's control.