Catwoman might be an unexpected ally. She has a love - hate relationship with Batman but could be swayed to help him if she sees the benefit or if Superman's actions somehow threaten her interests in Gotham. Also, Batman could potentially recruit some of the more tech - savvy villains from his rogues gallery. They could be persuaded to help him in exchange for reduced sentences or some other form of compensation.
Green Arrow could be an ally. He has his own set of skills and weapons that could be useful against Superman. His archery skills combined with some kryptonite - tipped arrows could be a formidable addition to Batman's side. And then there's the Flash. Although he is friends with Superman, in a story where Batman has a just cause, the Flash might be convinced to stay neutral or even help Batman subtly by creating distractions.
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.
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.
Well, the Black Ranger might also be a good match. He is a strong leader among the Power Rangers. Batman, being a natural leader himself, could respect the Black Ranger's leadership style. Together, they could lead a combined force of Gotham's vigilantes and the Power Rangers against a powerful enemy, coordinating their teams' efforts and using their combined resources to the fullest.
Wonder Woman could also be involved. She might be caught in the middle, trying to stop the fight at first. But if she realizes that Superman is being a threat for some reason, she could side with Batman, or at least not interfere in Batman's attempt to defeat Superman.
Lex Luthor. He's always looking for a way to take down Superman, and an apocalypse would be the perfect time for him to make his move. He could be using the chaos to build some sort of doomsday device or manipulate events to his advantage.
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.
Definitely the Bat - family. Robin, Nightwing, Batgirl, etc. would be there to pay their respects. Alfred, who has been like a father figure to Batman, would also be present. And of course, Commissioner Gordon, as he has been Batman's ally in the fight against crime in Gotham for a long time.
Sailor Mercury and Batman could be likely allies. Sailor Mercury is intelligent and tech - savvy, much like Batman. She could help him with any technological problems he might face in his fight against crime, while he could offer her his combat and detective expertise. For instance, if there was a villain using advanced technology to cause chaos in both their worlds, they could pool their knowledge to stop the bad guy.
Black Widow. She has a lot in common with Batman in terms of skills. Both are highly trained in combat, stealth, and espionage. They would understand each other's need for secrecy and their ability to operate in the shadows.
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.
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.