Another option could be a villain who is like Ra's al Ghul. This character could be interested in Izuku's newfound Batman - like abilities and try to recruit him to his side. Izuku would have to resist and fight against this powerful and manipulative enemy, using his sense of justice and his training inspired by Batman.
The Joker could be a great villain. Imagine if the Joker - like character emerged in the My Hero Academia world. Izuku, with his new Batman - inspired skills, would have to use his wits to outsmart this chaotic and unpredictable foe.
The Joker could be a main villain. He might see Izuku as a new plaything and try to break his spirit during his training with Batman.
In this fanfiction, Izuku could be inspired by Batman's lack of superpowers but still being a formidable hero. He may start training in more martial arts and stealth techniques, similar to Batman. And he could even create his own set of gadgets, like grappling hooks and smoke bombs, to aid him in combat and rescue missions.
Perhaps a new villain could emerge who specifically targets Izuku because of her new gender identity. This villain might see her as a symbol of change in the hero society that they don't want to happen. So they constantly attack her and try to break her spirit, thinking that if they can stop her, they can halt the progress of female heroes in general.
One possibility could be that Batman, after facing one too many betrayals in Gotham, decides to take a different path. Maybe the constant struggle against crime with little real change in the city makes him cynical. He could start using his skills and resources to control the underworld instead of fighting it. For example, he might start dictating which criminals can operate and where, creating a new order that is still dark but under his command.
He might be motivated by a sense of futility. After years of fighting crime and seeing no real end to it, he could think that the only way to bring about change is to control the criminal underworld himself. So, he becomes a villain to enforce his own version of order.
Maybe Thanos somehow discovers the wizarding world and decides he wants to add the power of magic to his collection of Infinity Stones. He could be the main villain, and Harry, with his understanding of both magic and his new Avengers - like abilities, would have to lead the fight against Thanos to protect both worlds.
It could be Kabuto. Since he has a lot of knowledge about medical ninjutsu and experiments, he might see Naruto's robotic form as a threat or something he can use for his own evil purposes. He could try to control Naruto's robotic functions and turn him against his friends.
Perhaps an old enemy of Batman who has made a deal with Cadmus. They combine their knowledge and resources. This could be someone like Mr. Freeze, who has found a way to use Cadmus' genetic engineering to make himself even more powerful. His new form and abilities would pose a great challenge for Batman Beyond.
Ra's al Ghul could also be a main villain. He might see the child of Batman and Catwoman as a potential weapon or a threat to his plans for Gotham. He could try to either recruit the child to his side or eliminate them, which would put Batman and Catwoman in a difficult position as they fight to protect their family from Ra's al Ghul's devious schemes.
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.