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.
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 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.
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 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 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.
One idea could be that Tony Stark tries to modernize Dunder Mifflin's technology. He'd be frustrated by the old - fashioned ways of the office. Another could be Thor working as a temp at the office and constantly getting into comical misunderstandings because of his Asgardian ways. Maybe Hulk could be the office's security guard, scaring off any unwanted visitors in a very Hulk - like manner.