A great plot could be that a villain has created a device that can swap the powers of the X - Men and Superman. So, Superman finds himself with mutant powers like telepathy, while some of the X - Men gain super strength and flight. They have to adapt to these new powers and work together to stop the villain from using this device for more evil purposes. This would also explore how the characters would react to having completely different powers and how they would use them in new ways.
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.
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 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 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 Superman and Invincible have to team up to stop an alien invasion that threatens both their worlds. The two heroes could initially clash due to their different methods but then learn from each other.
One idea could be that an alternate - universe version of Superman comes to their world. This could lead to a power struggle as both Supermen have different ideas on how to protect the city. Another plot could involve Lois getting superpowers temporarily and having to learn how to use them while also dealing with her regular reporting job.
Here's an idea. There could be a powerful magical artifact that surfaces in both cities. It has the power to change reality. Superman, being a man of science, is initially skeptical about its power. Batman, on the other hand, has seen enough strange things in Gotham to know it's dangerous. They have to overcome their differences in beliefs as they race against time to stop different factions in both cities who want to use the artifact for their own gain. Along the way, they also learn more about each other's worlds and form a stronger bond.
One idea could be that Superman gets transported to the Marvel universe during a freak interdimensional event. He teams up with the Avengers to fight a common enemy like Thanos, who has somehow obtained Kryptonite. Their combined powers and different strategies would make for an epic battle and an interesting exploration of how the two universes' heroes interact.
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.
A superman crossover with Wonder Woman would also be great. Maybe in a story where they have to travel to another dimension to stop an ancient evil. Their different powers and personalities would create a lot of interesting interactions, like Superman's more down - to - earth (even though he's from another planet) approach compared to Wonder Woman's Amazonian heritage.