The Riddler could be a great main antagonist. He loves to create complex puzzles and mysteries, which would be right up Sherlock Holmes' alley. And of course, Batman has had his run - ins with the Riddler in Gotham. Holmes' deductive skills and Batman's combat and detective skills would be put to the test trying to outwit the Riddler's convoluted plans.
Perhaps Moriarty could cross over into the Gotham world. Since he is Sherlock Holmes' arch - nemesis, it would be interesting to see how he would interact with Batman. Moriarty is a criminal mastermind, and his devious plans could easily spread to Gotham. Batman and Holmes would have to join forces to stop Moriarty from causing chaos in both their cities.
It could be a powerful sorcerer who has turned to the dark side. This sorcerer might be using his magic to manipulate events in Sherlock's world for his own gain. He could be creating illusions and false trails to throw Sherlock off, while also using his magic to fight against Doctor Strange.
Maybe there's a mystery that spans both London and Gotham. A villain is using a new kind of technology or drug that was first experimented with in London and is now being exploited in Gotham. Sherlock Holmes, having heard about Batman's reputation for dealing with such matters, travels to Gotham. They meet and initially clash due to their different methods. But as they start to share information, they realize that the villain is someone they both have a history with in some way. They then combine their efforts, Holmes with his mind and Batman with his gadgets and physical prowess, to stop the villain.
It could be Darkseid. He's a powerful and well - known villain in the DC universe. His goal of universal domination would put him in direct conflict with the Justice League and Batman's determination to protect Gotham and the world.
The main antagonist would be the Flashpoint Joker. In the Flashpoint universe, he is likely to be even more dangerous and unhinged. He could be targeting Batman directly or causing destruction that Batman feels responsible for stopping. His presence would drive the plot forward as Batman tries to outwit and stop him.
Lex Luthor would be a great antagonist. He could play on the differences between Batman and Superman, trying to turn them against each other while he pursues his own evil plans. Maybe he creates a situation where it seems like Superman is a threat to Gotham, causing Batman to be on high alert.
The theme of justice is also very common. Both Sherlock Holmes and Batman are dedicated to bringing criminals to justice. In fanfiction, they often team up or compete in the pursuit of this goal. They might have different ideas about what justice means exactly, but they both strive to make their respective worlds a better place by stopping the bad guys.
I think Harry Potter and Sherlock Holmes themselves would be the most interesting combination. Harry has this deep understanding of the magical world, its politics, and its secrets. Sherlock, on the other hand, has his brilliant deductive reasoning. When they come together, they can learn from each other. Harry can introduce Sherlock to magic, and Sherlock can teach Harry how to be more observant and logical in non - magical situations.
Ra's al Ghul could also serve as the main antagonist. He might have a new plan for Gotham that involves using Catwoman as a pawn. He could be aware of her relationship with Batman and try to use it to his advantage. Batman would have to not only save Gotham but also rescue Catwoman from Ra's al Ghul's clutches.
The Riddler could be a great main antagonist. He could use his intellect to create puzzles and traps that not only challenge Batman's detective skills but also the Flash's speed. For example, he could set up a series of time - locked puzzles where the Flash has to use his speed in a very specific way at specific times to unlock them, while Batman has to figure out the overall pattern of the puzzles.
Venom could be a main antagonist in this crossover. If Venom were to find his way to Gotham, he would be a formidable foe. His strength and aggression combined with his alien symbiote abilities would make him a tough opponent. Batman would have to rely on his gadgets and strategic thinking, while Spiderman, having prior experience with Venom, would have to use his knowledge of the symbiote to try and stop it. And Venom's desire to spread chaos and destruction would put both heroes in a difficult situation.