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.
In this fanfiction, Harry could be the last man on earth due to a powerful curse from an ancient dark wizard. He'd have to rely on his knowledge and skills that he learned at Hogwarts. He might try to communicate with the portraits in Hogwarts, hoping they can offer some guidance. As he delves deeper into the mystery, he discovers that there are some magical creatures that are also affected by this, and he has to find a way to save them all as well.
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.
It could be an ordinary guy. Just an average person who happened to survive whatever catastrophe wiped out the rest of humanity.
Another possibility is that Naruto himself could be his own antagonist in a sense. His loneliness and the weight of being the last man on earth could drive him to the brink of madness. He might have to fight his own inner demons, which could be manifested as a dark version of himself that wants to give up on the world and just let it decay.
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.
I think Batman has a good chance. He's a master strategist and is used to working alone. He has a wide array of gadgets and his detective skills would be very useful in a post - apocalyptic world. He could also use his knowledge of Gotham's underworld to survive.
It could be an ordinary guy. Just an average Joe who happened to be the one left. Maybe he was a simple office worker before the world changed.
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.