Perhaps Harry Potter and his friends are on a mission and they accidentally cross into Selene's world. They have to team up with Selene to fight against the lycans who see the wizards as new threats. Selene could teach them some of her combat skills while they introduce her to magic she's never seen before like spells for healing or protection.
One idea could be that Selene finds herself magically transported to the wizarding world of Harry Potter. She might initially be confused but then use her skills as a vampire to help in some sort of battle against dark wizards. For example, her enhanced speed and strength could give the Order of the Phoenix an edge in a fight.
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 that Hawkgirl somehow gets transported to the Harry Potter universe. Maybe she arrives during a Quidditch match and her flying skills astound everyone. She could then join forces with Harry and his friends to fight against the dark forces in Hogwarts, using her Nth metal mace and flight abilities in unique ways.
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.
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 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.
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.
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 the magic from Harry Potter is introduced into the world of Guilty Crown. For example, a Hogwarts student somehow ends up in the Guilty Crown universe and uses magic to combat the threats there. They could teach some of the characters basic spells like Lumos to help them in the dark environments.