Maybe the main villain is a mutant who has turned evil and has a grudge against both the wizarding world and normal mutants. He wants to destroy the balance between the two worlds. He sees Harry as a symbol of the wizarding world's power and Logan as a threat to his plans of mutant domination. So he sets out to eliminate them both.
A powerful demon from another realm could be the main villain. This demon has the ability to corrupt magic and mutate living beings. It sets its sights on Harry's magic and Logan's mutant abilities. It plans to use their powers to open a portal to its own realm and bring chaos to both the wizarding world and the world of mutants. Harry and Logan must put aside their differences and fight this demon together.
Well, it could be that Harry and Logan meet in a magical forest. Harry, being from his wizarding world, is intrigued by Logan's mutant abilities. Maybe they start by being cautious of each other, but then they realize they can help each other in some way, like Logan protecting Harry from some dark wizards who are after him for his magic, and Harry using his magic to heal Logan's wounds that won't heal on their own.
Voldemort could be a great villain. Imagine if he somehow discovers a way to enter Logan's world and starts using his dark magic to enslave mutants. Logan and Harry would have to put aside their differences in fighting styles and beliefs to take on Voldemort.
Dr. Eggman could team up with a Pokemon villain like Team Rocket. They could combine their technology and evil plans. Eggman might use Team Rocket's knowledge of Pokemon to capture strong Pokemon and use them in his machines, while Team Rocket could benefit from Eggman's advanced robotics to create more powerful devices for stealing Pokemon.
Obviously, Harry and the Grangers are the main characters. Harry is the famous wizard from the 'Harry Potter' series, and the Grangers are Hermione's parents, who are Muggles.
Maybe a corrupt businessman who discovers some ancient technology from the Old West that gives him superhuman abilities. He wants to use these abilities to take over Gotham and expand his business empire at any cost. He sees Batman as a threat to his plans and when the Lone Ranger shows up, he tries to get rid of them both. His greed and new - found powers make him a formidable foe for the two heroes.
It could be Voldemort who teams up with the Capitol. Voldemort is always looking for power and the Capitol has a lot of resources. Together they could create a really terrifying regime. They might use the Capitol's technology and Voldemort's dark magic to control people.
It could be Voldemort still. He would be really interested in Mega Man's technology and try to use it for his own evil purposes. Maybe he wants to combine magic and technology to create an unstoppable force.
There are often fanfics that put Harry Logan in different settings. For example, some might place him in a historical era, like the Victorian age. In this kind of fanfic, he has to navigate the different social norms and use his skills in a whole new context. There could also be a fanfic where he teams up with other characters from a related series to fight a common enemy.
Perhaps Sirius Black could also be involved. Sirius was Harry's godfather and was very much a part of Harry's life. His presence could add some interesting dynamics, like he could be the one who stumbles upon the magic that makes the meeting possible and then has to deal with the implications of Harry meeting his mother.
It could be a villain who wants to merge the Greek and Egyptian mythologies in a chaotic way. Maybe a powerful sorcerer who thinks that by combining the powers of the two worlds without any order, he can become the ultimate ruler.