There could be a sea witch or a wizard who has turned to piracy for evil purposes. This character might want to steal Harry's magic or use him in some dark ritual. They would constantly be trying to thwart Harry's pirate adventures and harm him or his new pirate friends.
One potential main antagonist could be a powerful pirate captain who sees Harry as a threat to his control over the seas. Maybe this captain has some dark magic powers as well.
The Ministry of Magic could also be an antagonist. They might not approve of Harry becoming a pirate and try to bring him back to the wizarding world against his will. They could send Aurors to stop him.
The traditional wizarding authorities could be antagonists. Since Fem Harry Potter is into pirate stuff which might be seen as unorthodox in the wizarding world, they could try to stop her from following this new path.
Perhaps the very magic that made Harry a god has a sort of negative side - effect. This could manifest as a shadowy entity within Harry that tries to take over his mind and use his powers for evil. So, in a way, this internal struggle could be the main antagonist in the story.
Some jealous students at Hogwarts could also act as antagonists. They might be envious of Harry's newfound allure and use underhanded tactics to try and make his life difficult.
Well, it's possible that a powerful and evil pirate lord could be the main antagonist in 'hermione is a pirate fanfiction'. This pirate lord might control a large part of the seas and sees Hermione as a threat to his dominance. He could have a large fleet and many ruthless henchmen. He might try to capture Hermione to either make her join his crew or to simply get rid of her because she is disrupting the order he has established in the pirate world.
It could be the navy. They see pirates as outlaws and would be determined to capture Percy and his crew. They might have better - equipped ships and more trained soldiers, making them a formidable foe for Percy and his fellow pirates.
In addition to Voldemort, there might be dark wizards who are jealous of Harry's new Hanyou powers. They could team up with some of the anti - Harry Hanyous to create a powerful alliance against him. This would force Harry to make some difficult choices about who to trust and how to fight back.
In this fanfiction, it could be that some of the Slytherin students who side with Voldemort become the main antagonists. They might be jealous of Harry's new power and try to expose him or cause trouble for him. For example, they could set traps in the forest hoping to catch Harry when he's in his deer form.
The Death Eaters could still be the main antagonists. Even if Harry is Lord Peverell, they would oppose him as he is still a threat to their dark ideology.
The Ministry of Magic could be a main antagonist. They have a history of being discriminatory towards werewolves. They might see Harry as a threat now that he's a werewolf and try to lock him up or restrict his movements. For example, they could pass new laws specifically targeting him, like making it illegal for him to attend Hogwarts as a werewolf.
Perhaps the traditional enemies of Harry in the wizarding world would also become more hostile. They might be scared of his new powers and try to take him down before he becomes too powerful. And there could be some powerful oni demon lords who want to control Harry and use his unique situation for their own gain.