A possible fanfiction could be that there is a magical mix - up that causes some of Harry Potter's spells to affect Fluttershy's world and vice versa. For example, the Patronus charm might transform into a pony - like form in Fluttershy's world. Fluttershy, being an expert on animals, could then study these new magical manifestations. Meanwhile, some of the magic from Equestria, like the ability to communicate with animals, could start to appear in the wizarding world, causing chaos and wonder among the wizards and witches.
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.
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.
Perhaps the Flying Dutchman has a powerful magical artifact on board that Voldemort wants to get his hands on. Harry Potter then has to race against Voldemort to reach the ship first. The ship's ghostly nature could pose a challenge as normal spells might not work as expected on it. For example, 'Apparition' might be disrupted near the ship due to its otherworldly magic.
Maybe there could be a crossover where some of the characters from Harry Potter, like Hermione, are fascinated by the technology and magic in Samurai Jack's world. They could study the different forms of magic there and try to incorporate it into their own magical knowledge. And in return, they could teach Jack some basic spells to use against Aku.