One idea could be that Shang Tsung somehow gets transported to the Harry Potter universe. He could pose as a new dark arts teacher at Hogwarts, using his shape - shifting abilities to deceive everyone. He might be secretly searching for a powerful magical artifact in the school that could enhance his own powers.
Perhaps there could be a magical experiment gone wrong that merges the powers of Shang Tsung and a Hogwarts student. This student then has to struggle with the new, dark powers while also trying to hide it from their friends and teachers. They might be lured by Shang Tsung's voice in their head, trying to convince them to embrace the dark side.
One idea could be a crossover where Naruto is transported to the Mortal Kombat universe and meets Shang Tsung. Naruto could learn some of Shang Tsung's shape - shifting abilities and use them in his own ninja world in a new way. Another idea is that Shang Tsung, being interested in Naruto's unique chakra, tries to steal it, leading to an epic battle between them.
The magic in Harry Potter has a certain set of rules and limitations. Shang Tsung's magic seems to be more unbridled. In a fanfiction, this contrast could lead to some great storylines. For instance, a young wizard or witch might be intrigued by Shang Tsung's power and try to learn from him, not realizing the danger. This could lead to a moral struggle within the character as they try to balance the new, dark knowledge with the good - natured magic they've been taught at Hogwarts.
One idea could be that Fluttershy somehow gets transported into the Harry Potter world. Maybe she arrives at Hogwarts as a new kind of magical creature that the students have never seen before. Her gentle nature might initially cause confusion among the more rowdy students, but she could gradually make friends with the likes of Luna Lovegood, who would be intrigued by her uniqueness.
Another concept could be that Harry Potter discovers he has a connection to Magneto's mutant powers. This might happen during a strange encounter with a dark magic object that unlocks a latent power within him. He then has to learn how to control these new abilities while also dealing with the threats in his own wizarding world, and he might seek out Magneto for guidance in a secret meeting across the boundaries of their two worlds.
One idea could be a crossover where Kakashi is summoned to the Harry Potter world by a dark magic spell gone wrong. He then uses his ninja skills and Sharingan to navigate the wizarding world, perhaps even teaching some Defense Against the Dark Arts classes with his unique combat knowledge.
Maybe in a fanfiction, Harry Potter and his friends accidentally stumble upon a hidden Cybertronian relic. This relic has some sort of power that attracts Megatron. Harry and his friends then have to defend the relic from Megatron while also trying to figure out what it does and how to use it to their advantage in the fight against Voldemort.
One idea could be a crossover where Harry Potter accidentally travels to the One Piece world and meets Whitebeard. He could learn about their different forms of magic and power, and together they face a new threat that combines the dark magic from his world and the powerful pirates in the One Piece world.
One idea could be a crossover where Harry Potter accidentally ends up in the world of Ranma 1/2. Maybe he's on a magical experiment gone wrong and lands in Nerima. He could use his magic to help Ranma deal with his curse, like creating a spell to keep him from changing into a girl when splashed with cold water.
Another concept could be a crossover where the magic in the Harry Potter universe has an unexpected effect on Android 18. For example, it could start to interact with her android systems in strange ways, giving her new powers or abilities that are a combination of magic and her android technology. This would lead to a whole new set of adventures as she tries to figure out what's happening to her.
One idea could be that Gandalf somehow gets transported to the Harry Potter universe. He could become a mentor to Harry, using his vast magical knowledge and wisdom from Middle - earth. Maybe he helps Harry understand some ancient magic that even Dumbledore wasn't fully aware of.