Well, perhaps there could be a situation where the Ministry of Magic tries to regulate mutant powers as they do with magic. Some mutants might resist this and seek refuge at Xavier's School for Gifted Youngsters. In the crossover, Professor McGonagall and Professor X could have an interesting exchange of teaching methods. McGonagall's strict yet nurturing style compared to Professor X's more accepting and guiding style. Also, imagine a character like Rogue being at Hogwarts. She could accidentally absorb the powers of a wizard, creating all sorts of chaos and a new mystery to solve.
One idea could be that the X - Men visit Hogwarts to teach the students about mutant powers and how to co - exist with those who are different. Another could be that Harry Potter discovers he has mutant abilities and has to navigate both the wizarding world and the world of mutants.
You could do a crossover with the Inhumans. The X Men and Inhumans have some similarities in terms of having special abilities. In the fanfiction, there could be a misunderstanding at first between the two groups. For example, Beast could be fascinated by the Inhuman biology while some of the more hot - headed X Men like Gambit might be a bit more aggressive in their initial interactions. Then they would have to work together to face a threat like an alien invasion.
Another idea is a crossover with the Star Trek universe. The X - Men could find themselves on a Starfleet ship. They might have to deal with the differences in cultures and technologies while also trying to stop Apocalypse from spreading his chaos across the galaxy.
A genetic experiment gone wrong could also be a great plot for the crossover. A mad scientist tries to combine mutant and super - soldier DNA. This creates a new breed of dangerous creatures. The X - Men, with their knowledge of mutants, and the Avengers, with their combat skills and high - tech resources, must work together to contain the threat. Jean Grey's telepathic powers could be crucial in finding the source of the experiment, while Iron Man uses his technology to develop a way to reverse the genetic changes.
One idea could be that the Hogwarts students are visited by Naruto and his friends. Naruto could show off his ninja skills, like the Shadow Clone Jutsu, which would amaze the wizards. The wizards, in turn, could introduce Naruto to magic like the Patronus Charm. Another plot could involve a common enemy that requires both the power of ninjutsu and magic to defeat. For example, a dark wizard who has also acquired some dark ninja arts.
One idea could be that Naruto is somehow transported to the wizarding world. He might attend Hogwarts and use his ninja skills in the wizarding duels. His chakra could be seen as a unique form of magic there.
One idea could be that Tonks gets involved in Harry's search for Horcruxes. Maybe her Metamorphmagus abilities help them in disguising and sneaking into places undetected. For example, she could transform into a Death Eater to infiltrate their meetings and gather information.
One idea could be that the Death Eaters in the Harry Potter world somehow gain access to Hollow powers from Bleach. This could create a new kind of dark magic that the Order of the Phoenix has to deal with. Another plot could involve Hogwarts students being sent to the Soul Society for a special training exchange, and they have to adapt to the different spiritual powers and rules there. And perhaps a powerful Hollows attacks Hogwarts and the wizards have to team up with the Soul Reapers to defeat it.
A great 'X Men Crossover Fanfic' idea could involve crossing over with the Buffy the Vampire Slayer universe. The X - Men could help Buffy and her gang fight some really powerful vampires that are immune to normal slayer weapons. Another idea is an X - Men and Doctor Who crossover. The Doctor could land in the X - Men's world and they could team up to stop some time - traveling villain who is trying to change mutant history. There could also be a crossover with the Ghostbusters. The X - Men and the Ghostbusters could work together to stop some mutant - created ghosts that are causing chaos in New York.
A cool plot could be that a new, extremely powerful mutant emerges who has the ability to control all forms of energy. This mutant's powers are so great that they start to disrupt the fabric of reality. The Avengers and the X - Men both realize that this mutant needs to be controlled or taught to manage their powers. However, different factions within both groups have different ideas on how to approach the situation. Some want to be more forceful, while others believe in a more diplomatic approach. This leads to internal conflicts within the combined group as they also battle external threats caused by the mutant's out - of - control powers.