One possible antagonist could be a jealous rival among the pirate gangs. This person might envy Harry Hook's sister's skills or popularity. Additionally, a corrupt official in the Isle of the Lost who wants to keep the status quo and sees her as a troublemaker could be an antagonist. Also, if there are any ancient curses or dark spirits on the isle, they could turn against her and try to stop her from achieving her goals.
The Foot Clan could be a main antagonist. They might see the baby sister as a way to get to the turtles, either by kidnapping her or using her to blackmail them. Another could be Shredder himself if he returns. He would surely not pass up the opportunity to use the baby sister against the turtles. And Baxter Stockman could also be an antagonist. He might be interested in using the baby sister for some of his mad - scientist experiments.
The Akatsuki could be the main antagonists. Since Naruto is an important target for them, and if Kurenai is now his sister, they might see her as an obstacle in their way. They could try to use their various powers and strategies to either capture Naruto or cause harm to both him and Kurenai.
Voldemort's remaining followers could be antagonists. They might target Harry's little sister thinking they can use her to get to Harry. They could try to kidnap her or use dark magic on her.
The Ministry of Magic could be the antagonists. Since Harry is in a gang, they might see him as a threat to the order of the wizarding world. They could send Aurors after him and his gang mates, trying to arrest them and break up the gang.
Voldemort's remaining followers could be the antagonists. They might see Harry's little sister as a way to get revenge on Harry or as a potential tool for their dark purposes.
The Thalmor could be great antagonists. Their strict control over magic and their anti - human beliefs could put them at odds with Harry. They might see his different form of magic as a threat to their power in Skyrim.
Some of the more traditional pure - blood families in the wizarding world could be antagonists. They might not approve of Harry, a half - blood, being involved with Pansy, and they could try to stop the pregnancy or break up the couple for the sake of 'pure - blood' ideals.
Voldemort or his followers could still be antagonists. They might not like the idea of Harry being under Euryale's protection as it could make him more powerful. Another possibility could be some creatures from Euryale's world who are against her taking in an outsider like Harry.
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.
It could be other members of the royal family who see Harry as a threat to their power or position. They might try to undermine him and prevent him from claiming his rightful place as king.