Alfred is always a likely ally. His knowledge and experience can provide valuable support to Batman. Also, Oracle (Barbara Gordon) could be an important ally, using her hacking skills to disrupt any technology Superman might use or to gather information.
Perhaps Batman has teamed up with some of Superman's other foes who have knowledge of his weaknesses. For example, Lex Luthor could provide Batman with technology or information that gives him the edge. Also, Batman might use psychological warfare on Superman, playing on his insecurities about being an alien among humans.
Lex Luthor is often an interesting character in such fanfictions. He might be the one pulling the strings behind the scenes, fueling Batman's distrust of Superman. Another could be Alfred. His wisdom and influence on Batman can add depth to the story. He might try to talk Batman out of fighting Superman or help him in a more covert way. And then there's Wonder Woman. She could be caught in the middle, trying to mediate between the two or having her own motives for getting involved in their conflict.
One popular plot could be that Batman discovers Superman has been mind - controlled by some villain. So, in order to save Superman and the world, Batman has to fight him. Another plot might involve a misunderstanding. Maybe some false information leads Batman to believe Superman is a threat to Gotham, and he takes action. There could also be a plot where Batman is pushed to his limits by some external force that makes him see Superman as an obstacle, and he uses his wits and skills to take on the Man of Steel.
Well, in a fanfic about Batman and Superman's friendship and fatherhood, they could be depicted as mentors to their sidekicks in a more fatherly way. Batman with Robin and Superman with Superboy perhaps. Their friendship might be tested as they balance their superhero duties and their newfound father - like roles.
One aspect of a Batman - Superman friendship fanfic could be how they overcome their differences. Batman is a dark, brooding vigilante while Superman is the all - American hero. Their friendship might start from a mutual respect for each other's abilities. For example, in a story, they could team up to fight a common enemy that neither could defeat alone. This would force them to rely on each other and learn about the other's strengths and weaknesses.
One common theme could be the exploration of their complex relationship in a more romantic or sexual context. Another might be the power dynamics between the two very powerful characters.
One common theme is the corruption of power. Maybe Superman's power has gone to his head, and Batman sees the need to stop him at all costs. Another could be a mind - control scenario where Superman is being controlled by an outside force and Batman has no other option.
One interesting Batman Superman fanfic could be about them teaming up to face a new, extremely powerful villain that neither could defeat alone. For example, a villain with the power to manipulate time. In the story, Batman's strategic mind and Superman's superpowers combine in unique ways to outwit the foe.
Lex Luthor is often a main antagonist. He might be the one who sets up the situation where Superman needs to be saved, like creating a powerful weapon or a devious plan to weaken Superman.