Perhaps a new type of creature that is neither from the Harry Potter world nor the Witch Hunter's world. It could be a result of some dark magic experiment gone wrong. This creature could have the ability to nullify magic in some ways, which would be a huge threat to both Harry and the Witch Hunter.
Perhaps a witch who has lost her family to witch hunters decides to take matters into her own hands. She disguises herself as a Muggle and tries to infiltrate the witch hunter's group to take revenge. This would make her a very interesting and complex main character.
There could be a non - human villain like a powerful and corrupted magical creature. It might have been awakened by the chaos in the wizarding world and decided to wipe out all the wizards except Harry, seeing him as a worthy opponent or a key to some greater power it desires.
One great 'Harry Potter and The Last Witch Hunter' fanfiction is 'The Crossover Chronicles'. It combines the magic of Harry Potter's world with the gritty, dark elements of The Last Witch Hunter. It has an interesting plot where Harry Potter teams up with the Witch Hunter to fight a new, powerful dark force that threatens both their worlds.
One of the most creative crossovers is the idea of a magical school in the world of The Last Witch Hunter, inspired by Hogwarts. In this fanfic, Witch Hunters' children start to attend this school, and they learn both traditional Witch Hunter skills and magic from the Harry Potter universe. It's a great mix of the two worlds' educational systems and magic concepts, and it shows how the two different cultures can blend together.
A fanfiction could explore what would happen if the magic from the Harry Potter universe was somehow combined with the powers of the Last Witch Hunter. For example, the Last Witch Hunter could gain the ability to use spells like Harry Potter, or Harry could get some of the unique skills of the Witch Hunter. This would lead to a whole new set of adventures and challenges for them both.
It could be a new character created by the fanfiction author. Maybe a powerful wizard who was once shunned by the wizarding community and now wants revenge by stealing magic.
A dark wizard who has merged the dark arts with Wonderland's magic could be the main villain. He might have created some sort of dark Wonderland where all the creatures are under his control, and Harry has to break this control to restore balance.
Perhaps the main villain is actually a corrupted version of a well - known character. For example, if Hermione was somehow influenced by the dark magic associated with the runestone path and turned against Harry. It would be a very unexpected and heart - wrenching twist, as she has always been such a loyal friend. But the power of the runestone path could be so strong that it changes her fundamental nature.
Maybe a new character, a Muggle - born wizard who was shunned by both the Muggle and wizarding worlds. This character, out of bitterness, decides to combine Muggle technology and magic to create the droid army and rule over both worlds. He would see Harry Potter and his friends as the main obstacles to his grand plan.
It could be someone new, a dark wizard who has learned about Naruto's reincarnation and wants to use his power for evil. This new villain might try to manipulate Naruto into using his chakra in a wrong way. Or perhaps it could be a combination of Voldemort and some of Naruto's old enemies from his previous life who somehow find a way to merge their powers in the Harry Potter world.