One way to explain it could be through the influence of a powerful dark object. Maybe he stumbles upon an ancient and cursed artifact that slowly corrupts his mind. It starts to make him see the world in a different, more self - serving way, and eventually turns him into a villain.
One way to explain Ruby's transformation into a Grimm in fanfiction could be through some kind of experimental magic gone wrong. Maybe she was exposed to a new type of spell that was supposed to enhance her powers but instead turned her into a Grimm.
Voldemort could still be a potential villain even in 'Harry Potter leader fanfiction'. Maybe he returns in a different form or has some followers who are still causing trouble while Harry is trying to lead the wizarding world into a new future.
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.
A possible main villain could be a dark wizard who has learned some of the criminal tactics from the Detective Conan world. He could be using both magic and devious non - magical schemes to cause chaos. For instance, he might use spells to steal valuable items and then use the underworld connections in Conan's world to sell them.
Maybe the main villain could be a corrupted Hogwarts professor. This professor could be secretly teaching dark magic to students and when Harry's child discovers this, they become the target. The professor wants to stop the child from revealing their dark secrets and will go to great lengths to do so, making them a formidable villain in the fanfiction.
A new dark wizard or witch could be the villain. Maybe they are jealous of Harry's fame and power. They study dark arts intensively and develop a spell to trap Harry in his mind. This new villain might not be directly related to Voldemort but has their own evil motives, like ruling the wizarding world by getting rid of Harry who is seen as a major obstacle.
A possible main villain could be an ancient sorcerer from the new dimension who has been awakened from a long slumber. He's enraged that the wizarding world has been interfering with his dimension's magic, and decides to take revenge on Harry Potter's world. He has powers that are unknown to the normal wizarding world, like the ability to control time in his dimension, which makes him a formidable foe.
It could be a rogue wizard who has a vendetta against the Dursleys for some reason and decides to attack when Harry is home alone. Maybe the Dursleys once unknowingly wronged this wizard's family, and he wants revenge.
It could be a new character that is a combination of a dark wizard and a Hollow. This creature would be able to use both dark magic and Hollow abilities. It would target both Hogwarts students and Soul Reapers. Ichigo and Harry would have to figure out its weaknesses, which would be a difficult task as it has powers from two very different universes.