In some versions of the 'naruto destroys konoha fanfic', an external force could be the real antagonist. They could manipulate Naruto into believing that Konoha is the problem. For example, a powerful ninja from another village could use genjutsu on Naruto, making Konoha seem like a threat to the world, and Naruto would then try to destroy it, while the real enemy is the one using the genjutsu.
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.
The ANBU black ops could also play the role of antagonists. They are the ones who carry out the village's more secretive and sometimes morally gray missions. If they are ordered to hunt Naruto down unjustly, they would be in Naruto's way and could be the reason for his violent reaction towards Konoha.
The elders of Konoha could be the main antagonists. They are often shown to be power - hungry and willing to do whatever it takes to maintain their control over the village. They might see Naruto as a threat to their authority and decide to betray him. Another possibility is Danzo. He has always had his own agenda and has been shown to be ruthless in achieving his goals. He could easily be the one behind the betrayal of Naruto in a fanfic.
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 elders of Konoha could be the main antagonists. They are often the ones making the big decisions in the village. If Naruto is seeking revenge, it could be because of their actions, like how they treated him when he was a child or how they might have hidden important information from him.
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.
Maybe Danzo could be a major antagonist. He's always been a shadowy figure with his own agendas. He might see Naruto as a threat to his secret operations and influence in Konoha, and thus play a key role in getting Naruto executed.
There could also be some ancient monsters or spirits that are tied to Olympus' existence. They might rise up to defend it because their own survival is linked to the continued existence of Olympus. These could be powerful beings that Percy has never faced before, adding an extra layer of danger to his quest to destroy Olympus.
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.
Maybe the hidden organizations within Konoha that work in the shadows. They could have been involved in some plot against Naruto that led to his decision for revenge. They would be the ones trying to stop Naruto from exposing their secrets and exacting his revenge on the village as a whole.