Another possibility is that it could be a corrupted version of fem Bowser herself. Maybe the dark magic in the Harry Potter world starts to influence her, and she becomes a danger to both the wizarding world and her newfound friends. Harry and his friends would then have to find a way to bring her back to her original self before she causes too much destruction.
Maybe a new character that is created specifically for this fanfiction. This character could be jealous of the attention fem Bowser is getting from both the wizarding world and Harry Potter's group. They could start causing trouble and trying to turn everyone against fem Bowser. This new antagonist could also have some connection to Bowser's original world, perhaps an enemy from there who has followed her to the Harry Potter universe.
In a 'Harry Potter x fem Bowser' fanfiction, it could be that fem Bowser is a part of a prophecy in the Harry Potter world. The prophecy states that a powerful being from another realm will come to either save or destroy the wizarding world. Harry and his friends are initially skeptical but soon realize that she has her own reasons for being there. She could be on a quest in her own world that has some connection to the events in the Harry Potter universe, and together they must figure out how to use her presence to their advantage.
It could be a powerful dark wizard who is also involved in the hitman business. This wizard might see fem Harry Potter as a threat to his operations.
It could be a dark wizard who wants to take over the farm for its magical properties. Maybe there's a hidden well of ancient magic there that he desires.
The mummy itself could be the main antagonist. It could be a mummy that was once an evil sorcerer in ancient Egypt, and now that it has been awakened, it wants to spread its dark magic and rule over both the Muggle and wizarding worlds.
Obviously, Slenderman could be the main antagonist. His spooky nature and his ability to cause fear and disappearances would make him a perfect fit for the role. He could be trying to spread his influence over the wizarding world, which would put him in direct conflict with Harry and his friends.
It could be Voldemort still. Imagine Ares coming into the Harry Potter world, and Voldemort seeing this as a threat to his own power. He would try to either eliminate Ares or use him for his own dark purposes. Ares, on the other hand, may not take kindly to Voldemort's evil ways and so they become enemies, with Harry in the middle trying to defeat Voldemort while also keeping Ares in check.
It could still be Voldemort. Since he is the main villain in the original Harry Potter series, in this fanfiction he would see the Goddess Lemon as a threat to his plans of taking over the wizarding world. He might try to eliminate her before she can fully use her powers to help Harry and the Order of the Phoenix.
Another option could be a corrupted version of Merlin. What if he was turned evil by some dark magic? He would know all the secrets of both the Arthurian and wizarding worlds. He could use this knowledge to create chaos and try to rule over both. Harry and the good knights of Arthur would have to find a way to reverse his corruption.
It could be an ancient evil spirit that was sealed away by Fem Hashirama in the past. Now that she has resurfaced in the Naruto - era, the spirit is also awakened. This spirit wants to destroy the world that Fem Hashirama once protected and Naruto, being the hero of his time, stands in its way along with Fem Hashirama.
The Volturi could be a main antagonist. They might see the intrusion of the wizarding world into their territory as a threat to their power and secrecy. They could try to eliminate Harry Potter and Charlie Swan to protect their vampire - centric world in Forks.