Another possibility is that there could be a new character introduced in the fanfiction, a mastermind who manipulates Harry into believing that his family is a threat. This new character could be the main antagonist.
Maybe it's a family member who has been hiding their true nature all along. For example, if a family member turns out to be a secret Death Eater or has some other malicious intent, Harry's reaction to this discovery could lead to the 'destruction' of the family, making that family member the antagonist in the story.
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.
Some of Harry's friends could also be antagonists in this fanfiction. They might not understand his reasons for wanting to destroy the wizarding world and try to stop him. For example, Hermione, with her love for knowledge and the wizarding world's institutions like Hogwarts, would probably try to reason with Harry and, if that fails, might even fight against him to protect the world she loves.
Voldemort would likely still be a main antagonist. He is the one who poses the initial threat to Harry in the first place. His followers, like the Death Eaters, could also be major antagonists, constantly trying to get to Harry even after the Potter family has rescued him.
It could be Orochimaru. He has always been interested in power and the secrets of the tailed beasts. So, he might see Naruto and the Jinchuuriki family as a source of great power to experiment on or steal from.
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 some hidden members of Naruto's family itself. Maybe there are relatives who have been manipulating things from the shadows and their actions led Naruto to believe he needs to take revenge on the family as a whole.
The elders of his family or clan could be the main antagonists. They might have exiled Naruto in the first place due to some old - fashioned beliefs or fear of his power. Throughout the fanfiction, they could try to stop Naruto from finding out the truth or coming back to the clan.
His family members themselves could potentially be antagonists in a sense. If Naruto is rejecting them, there could be some family members who try to stop him from leaving or try to change his mind forcefully. They might see his rejection as a threat to the family's reputation or unity.
It could be Draco Malfoy. He might not like the idea of Harry getting a second chance at the OWLS and tries to sabotage him. Maybe he spreads rumors about Harry not being worthy of a retake.
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.