The village elders or certain hidden factions within the village could be antagonists. If Naruto turns dark because of their actions against him, they would naturally be in opposition to him as he seeks revenge or tries to change the village in a way they don't want.
Some of the teachers at U.A. might also be antagonists. They could be secretly working for an organization that wants to control Izuku's powers for their own evil purposes. They would pretend to be helpful while actually setting traps and spreading misinformation about him.
The Ministry of Magic could be antagonists. If they start to oppress those with different views, including Harry, it could drive him towards darkness. Their corrupt and unjust actions might make Harry think that the only way to fight back is by using dark magic.
Even some of Naruto's former friends could become antagonists in this type of fanfiction. If they are influenced by false information or some external force, they could turn against Naruto, which would further fuel his descent into darkness.
It could be the Death Eaters who see Harry's new - found mastery of darkness as a threat to their own power and ideology. They might try to either recruit him or destroy him. Voldemort himself could be an antagonist, feeling that Harry is encroaching on his territory as the most powerful dark wizard.
The obvious choice would be the Prince of Darkness himself. He could be a powerful being with the ability to manipulate shadows and dark magic, constantly trying to draw Percy to the dark side.
The villagers themselves could be the main antagonists. Since Naruto has given in to hate, he may see the villagers' past mistreatment of him as unforgivable. Their judgmental and often cruel behavior towards him in his childhood could now be the reason he turns against them, making them the antagonists in this new narrative.
A powerful wizard who wants to use the 'lady of darkness' powers for his own evil gains could be an antagonist. He might try to manipulate her into doing his bidding.
The Sound Ninjas could be great antagonists. They could use their own unique parkour - like skills to try and stop Naruto. They might be chasing him through the forest, and Naruto has to use his parkour skills to outmaneuver them.
Maybe some corrupt officials within the prison system itself. They oppose Naruto's more humane and reform - focused approach to prison management. They might try to undermine him at every turn, for example, by cutting off resources or spreading false rumors about him among the prisoners.
Maybe a group of dark - type Pokémon that have banded together and are trying to overthrow Arceus. They view Naruto as an easy target at first, but quickly realize he is a formidable opponent with his ninja skills and new Pokémon - related powers. They would constantly try to undermine Naruto and his efforts to protect the Pokémon world.