A cool plot could be that a mutant with the power to teleport accidentally ends up in Smallville. This mutant could bring some news about a new threat that is targeting both mutants and Kryptonians. Clark and the X - Men then have to figure out who this new enemy is and how to stop them. Or perhaps a young mutant runs away from the Xavier Institute and ends up in Smallville, where Clark helps them understand and control their powers better, but this draws the ire of some anti - mutant groups who then target Smallville as well.
One idea could be that the kryptonite in Smallville starts to affect the mutants in strange ways. Maybe it suppresses or enhances their powers in unexpected manners. For example, Wolverine's healing factor could be slowed down by kryptonite exposure, leading to a real threat when he gets injured. Another plot could involve Lex Luthor getting his hands on some mutant DNA and trying to create his own super - soldiers, which would draw the attention of the X - Men. They could team up with Clark Kent to stop Luthor's evil plans.
One idea could be that the alien technology from Roswell somehow finds its way to Smallville. The kryptonite in Smallville could have an unexpected reaction with the alien biology from Roswell. Maybe the characters from Roswell come to Smallville in search of a new energy source and end up getting involved with the local mysteries and the Kents.
One idea could be that Batman visits Smallville to investigate some strange technology that has been showing up in Gotham and has ties to LuthorCorp. He teams up with Clark Kent, who is still in his early days of understanding his powers. They could have a cool dynamic where Batman is initially suspicious of Clark but then realizes he's a powerful ally.
Perhaps there could be a story where Lex Luthor somehow gets hold of some of Arrow's technology and Clark has to work with Oliver to retrieve it. They would have to combine their skills, Clark's superpowers and Oliver's archery and combat expertise.
Perhaps in the fanfiction, there's a time - traveling aspect. Barry's time - traveling experiments go wrong and he ends up in Smallville during Clark's high school years. They have to figure out how to get Barry back to his own time while also dealing with a villain who is trying to change the future by targeting Clark in the past. This could involve both of them learning about each other's powers and how to work together effectively.
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.
One idea could be that Superman is somehow transported to the X - Men's universe. He teams up with the X - Men to fight a common enemy like a powerful mutant who has the ability to nullify Superman's powers on a large scale. They have to figure out how to combine their skills and powers to overcome this threat.
One plot idea could be that the One Ring somehow finds its way into the X - Men universe. Maybe Magneto senses its power and wants to use it for his own purposes, believing it could give him ultimate control over mutants and humans alike. The X - Men, on the other hand, realize the danger of the Ring and try to stop Magneto from getting his hands on it. Another idea is that some of the LOTR characters are reincarnated as mutants. For example, Aragorn could be a mutant with enhanced leadership abilities and physical prowess, and he teams up with the X - Men to fight a common enemy that threatens both Middle - earth and the mutant world.
One idea could be that the X - Men and Spiderman team up to fight a common enemy like Magneto who has joined forces with some of Spiderman's foes, such as Doctor Octopus. They'd have to combine their powers and skills to take on this powerful alliance.
One idea could be that the Winchesters end up in Smallville while hunting a demon that has some connection to LuthorCorp's experiments. Maybe the demon is using the kryptonite there for its evil deeds. Another could be that Clark Kent discovers the existence of the supernatural world through Sam and Dean. He could initially be skeptical but then realize there are threats that even his powers might not be enough to handle.
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.