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. He is a powerful and menacing villain. In an apocalypse, he might see it as an opportunity to finally conquer Earth. He could be behind the events that led to the apocalypse in the first place, or he could be swooping in to take advantage of the weakened state of the planet.
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.
I really like the fanfic 'Apocalypse's Aftermath'. In this story, the world is in ruins after the events of the Batman Superman Apocalypse. It focuses on how the remaining heroes, including Batman and Superman, are trying to rebuild society while also dealing with the new threats that have emerged from the chaos. It's a very character - driven story.
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.
The popularity of 'Batman Superman Apocalypse' fanfiction comes from the iconic nature of the characters. Batman and Superman are two of the most well - known superheroes. People love to explore different scenarios where they interact during an apocalypse, which is a very dramatic and action - packed setting.
Lex Luthor would be a great choice. He's Superman's long - time nemesis. He could form an alliance with some of Batman's foes like the Joker. Luthor could use his intelligence and resources to create a plan that only Superman and Batman together could stop.
Harley Quinn is an obvious choice. Her obsessive love for the Joker could be transferred to Batman in a fanfiction harem scenario. She's unpredictable and could add a lot of chaos and humor to the group. Then there's Poison Ivy. Her connection to nature and her alluring charm would make her a likely candidate. She could use her plants to protect the harem or create a private sanctuary for them.
The comic features a major conflict between Batman and Superman as they face an apocalyptic threat. It's full of action and intense moments.
In a fanfiction, perhaps there's an apocalypse scenario where Superman is infected with some kind of kryptonite - based virus that makes him go berserk. Batman has to find a cure while also keeping Superman from causing too much damage. At the same time, they are dealing with the general chaos of the apocalypse, like gangs taking over the city and other villains trying to take advantage of the situation.
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.