One common theme is the contrast between their powers and personalities. Superman is all - powerful and has a more optimistic view, while Batman is a normal human with great skills and a darker, more brooding nature. Their interactions based on these differences are often explored.
Brainiac could also work well. He is an android with an insatiable thirst for knowledge and a penchant for collecting and destroying planets. In a crossover, he could target Earth, specifically Gotham and Metropolis. His advanced technology would pose a major challenge to both Superman and Batman. Superman's super - powers would be put to the test against Brainiac's powerful defenses, and Batman would need to use his wits to find a weakness in Brainiac's systems, leading to an exciting and complex story.
One great piece of superman and batman crossover fanfiction is 'World's Finest: The Darkest Night'. It explores a scenario where Superman and Batman have to face a new, extremely powerful villain that threatens both Gotham and Metropolis. The story does a great job of showing how their different powers and personalities work together in a fight.
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 possible reason could be mind control. Maybe some villain has taken over Superman's mind and made him do it. Another reason might be a fundamental difference in their ideologies that has escalated to the point of no return.
One idea could be that a powerful new villain emerges who has the ability to manipulate both Batman and Superman's minds. This forces them to fight against each other while the real enemy is pulling the strings. Another could be a situation where Gotham and Metropolis are in a territorial dispute, and Batman and Superman initially take sides based on their cities, but then realize they've been played.
Darkseid is another option. His power and his desire to conquer Earth could bring Batman and Superman together. He could target both Metropolis and Gotham, and his presence would require the two heroes to combine their skills. Batman's strategic mind and Superman's brute strength would be needed to face this powerful foe.
One idea could be that Batman and Superman are forced to team up against a common enemy from another dimension. This enemy has the power to manipulate the minds of the citizens of Metropolis and Gotham, making them turn on their heroes. Batman uses his detective skills to find the source of the mind control, while Superman has to hold off the hordes of brainwashed civilians.
Lois Lane is often a popular character. In fanfiction, she might play a crucial role in mediating between Batman and Superman or getting involved in their adventures in a more hands - on way, using her investigative journalism skills.
Alfred Pennyworth is quite popular too. He can offer his wisdom and support to Batman, and his interactions with Superman can be both humorous and heartwarming. He's like the glue that holds things together in the Batcave, and his presence can bring a sense of home to the story.