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.
One idea could be Deadpool trying to join the X - Men but constantly messing things up with his unorthodox methods. For example, he might start a fight with the wrong mutant during a training session because he misread the situation.
One idea could be a battle against a common enemy that is too powerful for either the Avengers or the X - Men alone. For example, a powerful alien race that wants to enslave mutants and humans alike. The two groups would have to combine their unique powers and skills to defeat this enemy. Another plot could involve a misunderstanding between the two teams that leads to a brief skirmish before they realize they are on the same side. For instance, the Avengers might mistake the X - Men's actions as a threat to humanity when in fact they are trying to protect a mutant from a rogue government agency.
One idea could be that a powerful cosmic entity threatens both the Avengers' world and the X - Men's. So they have to combine their forces. For example, Iron Man could work with Beast to develop new tech to counter the entity's energy. Another could be a mutant - hating villain who uses some of the Avengers' tech to target mutants, forcing the two groups to team up to stop him.
One idea could be that a powerful mutant villain emerges who is able to manipulate time. This causes disruptions in both the X - Men and Avengers' universes. The X - Men, with their knowledge of mutants, and the Avengers, with their vast resources and superpowers, have to team up to stop this villain. They start off distrusting each other, especially because the Avengers are sometimes seen as anti - mutant by some in the X - Men world. But as they face challenges together, they learn to work as one.
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 an OC with the power to manipulate time. They could be a new recruit to the X - Men and struggle with using their power responsibly. For example, they might accidentally send a teammate into a different time period and have to figure out how to bring them back.
A cool 'X Men Ascension' fanfic idea would be to set the story in an alternate universe. Maybe in this universe, the roles are reversed, and the mutants are the ones in power while the humans are the ones feared. How would the X - Men handle this situation? Would they be more benevolent rulers or would power corrupt them? It could be a really interesting exploration of the 'X Men Ascension' concept.
A Naruto x One Piece crossover would also be cool. Naruto could end up on the Grand Line and team up with the Straw Hat Pirates. His ability to create shadow clones could be useful in battles against other pirates, and he might learn some new skills from Luffy and the crew.