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.
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.
It could be in a self-defense situation when the basilisk poses an immediate threat to him or his friends in Hogsmeade.
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.
Yes, it could be. Hogwarts is a very important place in the Harry Potter world, and Harry Potter is the main hero. So it makes sense that protecting Hogwarts by Harry is a popular theme.
In some fanfictions, there could be other dark wizards or witches who are allied with Voldemort or have their own reasons for wanting to harm Harry. Snape would have to protect Harry from these various threats as well. For example, some Death Eaters might try to take matters into their own hands and go after Harry without Voldemort's direct orders.
One common theme is redemption. Slytherins are often seen as the 'bad guys' in the original series, so protecting Harry gives them a chance at redemption. For example, they might be trying to make up for past wrongs or the actions of other Slytherins.