Often, it could be Death Eaters or their remnants. They might be after the same secrets or power sources in Godric's Hollow as Harry and Hermione.
Sometimes, there could be a new dark wizard or witch who has emerged and is targeting Godric's Hollow for its magical significance. This character might be jealous of Harry's fame and Hermione's intelligence and see them as obstacles to getting what they want from the place. They could use all kinds of dark magic to try and stop Harry and Hermione from achieving their goals.
One possible plotline could be Harry and Hermione exploring the hidden secrets of Godric's Hollow. Maybe they discover an ancient magic there that was left by Godric Gryffindor himself. Another could be them facing some dark forces that are also interested in the secrets of the place.
Often, the goblins can be antagonists. If they have their own motives that conflict with Harry and Hermione's, like protecting a dark secret in the vaults or trying to take advantage of the situation for their own gain. Another possible antagonist could be a Death Eater who has infiltrated Gringotts to either steal something important or to ambush Harry and Hermione.
Often, it could be Death Eaters. They are the main villains in the Harry Potter series, so it makes sense for them to be antagonists in fanfiction where Harry and Hermione need to escape.
Some dark wizards or witches who are looking for power might see Harry as a tool or a target. If they think they can harness the power of a hollow - Harry, they would try to capture him. This could lead to many battles and challenges for Harry as he grows up in this strange new form.
Well, in some fanfictions, Voldemort or his remaining Death Eaters could be antagonists. They might see Harry and Hermione's relationship as a threat to their plans. For example, if they think that a united Harry and Hermione are more powerful and could foil their dark schemes more easily.
Another possibility is that there could be some corrupted magical authorities who don't want Harry and Hermione to be in Forks for some political reasons. They could send their minions to create trouble for Harry and Hermione, making them the main antagonists in the fanfiction.
It could be the Ministry of Magic if they turn corrupt or power - hungry. They might see Harry and Hermione as a threat to their authority and try to stop them at all costs. Another possible antagonist could be a dark wizard or group of dark wizards who are using the chaos in the wizarding world to their advantage and Harry and Hermione are the only ones standing in their way.
Sometimes, the pure - blood supremacist families who oppose any changes to the traditional wizarding hierarchy can be antagonists. They see Harry and Hermione's attempts to take control and make things more equal as a threat to their long - held power and privilege. They may use their influence in the Ministry of Magic or other institutions to try and stop Harry and Hermione.
Often, it could be dark wizards or witches who are envious of Hermione's status as the heir. They might want to take over Hogwarts themselves or steal the power that comes with being the heir. For example, a powerful dark wizard who has been in hiding for years might emerge to challenge Hermione.
In some fanfictions, it could be the Death Eaters still causing trouble. They might be targeting Harry and Hermione specifically during their 6th year, trying to disrupt their studies or even harm them.