A group of dark creatures, like Dementors that have gone rogue, could be the antagonists. They might be drawn to the emotions of the villagers in Hogsmeade. Harry would have to use his ability to produce a powerful Patronus to keep them at bay and protect the village from their soul - sucking presence.
It could be a new dark wizard who wants to make a name for himself. He sees Hogsmeade as an easy target to show his power. He starts by causing small disruptions like making objects in the shops move on their own and then escalates to more dangerous attacks that Harry has to stop.
Well, perhaps in the fanfiction, Harry could be protecting Hogsmeade from a group of dark wizards who are trying to steal some powerful magical artifacts hidden in the village. He might use his Patronus charm to fend them off and rally the villagers to fight back.
It could be the White Walkers if this is a crossover fanfic set in the Game of Thrones universe. They are a huge threat to the Starks in their own world, and Harry Potter would have to find a way to stop them.
In many cases, the main antagonists can be other Slytherins who still hold grudges against Harry or are loyal to the pure - blood supremacist ideology. They might see Harry as a threat to their way of life. Also, some Death Eaters can be antagonists. They target Harry because of his role in Voldemort's downfall and would stop at nothing to get to him.
One possible consequence could be a lot of chaos and panic among the students and residents. With Hogsmeade being a popular place for Hogwarts students to visit, an attack would surely terrify them. Some students might get separated from their friends or get injured. The safety of Hogwarts itself could also be in jeopardy as Hogsmeade is so close. The local businesses in Hogsmeade would likely suffer great losses, and it might take a long time for the place to recover its former charm and prosperity.
It could be the Death Eaters. They are always looking for ways to cause chaos and undermine the wizarding world. Hogsmeade, being a place full of both students and ordinary wizards, would be a prime target for them to strike fear into the hearts of everyone. Another possibility could be some rogue dark wizards who are not directly affiliated with Voldemort but have their own evil agendas.
One possible scenario could be that Harry needs Hermione's help with something specific in Hogsmeade. Maybe he wants to research a certain magical item in one of the shops there, like Zonko's Joke Shop for some prank - related research or Honeydukes for information on a particular sweet that has a magical property. He knows Hermione is the best person to go with as she's so knowledgeable about all things magical.
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.
The Death Eaters could be the antagonists. Even though Voldemort is gone, some of his followers might not want Harry to succeed in building a starship as they fear it could bring more power to Harry and his friends, and they still hold grudges against him.
The Ministry of Magic could be a major antagonist. Since necromancy is considered a dark art, they would try to stop Harry at all costs. They might send Aurors after him or try to expel him from Hogwarts.
Some pure - blood supremacist wizards might oppose Harry. They may not like the idea of a half - blood like Harry having so much control over a city and could try to create unrest. Also, there could be some non - magical criminals who target the city because of its new magical elements under Harry's leadership.