One idea could be a crossover where Harry Potter characters are transported to the Ninja Gaiden world. For example, Harry could find himself in a situation where he has to learn ninja skills to survive. He might team up with Ryu Hayabusa and they could fight against the Death Eaters and the demons from Ninja Gaiden together. This would create an interesting dynamic as Harry's magic and Ryu's ninja abilities would complement each other in combat.
Another concept could be a story in which the magic from Harry Potter is introduced to the Ninja Gaiden universe. The ninjas could start to study magic, and it could change the way they fight. Maybe some of the Hogwarts professors could be invited to teach at a ninja academy. This would lead to a lot of cultural clashes and interesting interactions between the two groups of characters.
First, you need to have a solid understanding of both universes. Know the rules of magic in Harry Potter and the combat styles and lore in Ninja Gaiden. Then, create an engaging plot. It could be a simple quest or a complex battle against a combined evil. Next, develop your characters well. Show how the Harry Potter characters react to the Ninja Gaiden world and vice versa. For example, how would Hermione approach learning ninja skills? Finally, write in a way that keeps the readers interested, with good pacing and description.
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.