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.
One reason could be that Naruto has seen too much death and destruction in Konoha. His 'godlike' state might make him think that the only way to end all the suffering is to destroy the root cause, which is Konoha. He may believe that Konoha's system is so broken that it can't be fixed and needs to be completely eradicated.
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.
In a 'naruto destroys konoha fanfic', one possible plot could be that Naruto is pushed to the edge by the villagers' constant mistreatment and the hidden secrets of Konoha's leadership. He discovers some dark deeds that the village elders have been involved in, like using him as a pawn without his knowledge. This betrayal could fuel his anger and lead him to decide to take revenge on Konoha.
One possible plot could be that Naruto is somehow mind - controlled by a powerful enemy who forces him to turn on Konoha. Maybe the enemy has a special jutsu that can manipulate Naruto's emotions and memories, making him believe that Konoha has wronged him in some way.
In such a fanfiction, it would be a very dark and alternative take. Naruto, being godlike, might have been pushed to the edge by something in Konoha, like betrayal or unjust treatment. Maybe he discovers some dark secrets about the village leaders that make him snap.
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.
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.
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 Hokage, whoever it is at the time, would see Naruto's actions as a major threat. They would likely assemble the ninja forces to defend Konoha. But there would also be a part of them that would wonder what drove Naruto to this. Kakashi, for example, would be conflicted. He has a deep bond with Naruto, but he also has a duty to protect Konoha. So he would try to find a way to end this without harming Naruto too much.