It could be a new villain who has a vendetta against both Batman's family (including Batmom) and the Justice League. Maybe a powerful criminal mastermind who has studied both sides and found their weaknesses.
Perhaps the main antagonist could be a rogue member of the Justice League who has turned evil. Batmom would then be in a unique position to try and bring this former hero back to the light while also protecting the rest of the League. This would create a lot of internal conflict within the story as the League has to deal with one of their own. And Batmom's relationship with Batman might play a crucial role in understanding how to handle this situation.
In this fanfiction, Batmom might show her unique skills and knowledge. Maybe she helps the Justice League with some insider information about Gotham's villains. She could also form interesting relationships with the members of the Justice League, like a motherly figure providing advice and support.
The Riddler could be a great antagonist. He might have a grand scheme that not only affects Gotham but also has implications for the Justice League's interests. His riddles could stump both Robin and the League members, forcing them to work together to decipher his plans.
It could be the Joker. Since he's one of Batgirl's main foes in Gotham, his chaotic nature would pose a great threat to the Justice League as well when they enter Gotham's affairs.
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.
A tech - genius named Techno - Tyrant. He could be a former game developer who turned evil after his creations were rejected. He uses his knowledge of gaming mechanics and virtual reality to create dangerous traps for the Justice League.
Lex Luthor could be a great main antagonist. He might see Izuku as a threat to his plans, especially if Izuku's unique abilities and sense of justice start to disrupt Luthor's schemes in the combined universe. Luthor could try to manipulate events to turn the Justice League against Izuku or find a way to steal Izuku's power for himself.
It could be a new villain who has a grudge against the Justice League. Maybe someone whose family was affected by the League's actions in the past. This villain would be very smart and powerful, creating elaborate traps for the League members.
The Joker could be a great antagonist. Imagine him being intrigued by the formation of the Justice League after Batman's start in 'Batman Begins'. He could see it as a new toy to play with and start causing chaos in a way that targets both Batman's Gotham roots and the League as a whole. He might use his mind games to try and turn the League members against each other.
The League of Shadows could be a great antagonist. They might see Young Justice as a threat to their plans in the world and Batgirl as an obstacle in Gotham. They could try to manipulate situations to make Young Justice and Batgirl turn against each other while they carry out their own devious plans, like releasing a dangerous virus in a major city.
It could be Eggman. He might team up with some of the Justice League's villains, like Lex Luthor. Eggman could bring his mechanical creations and knowledge of chaos emeralds, while Luthor provides his strategic mind and resources. Together, they could pose a huge threat to both Sonic and the Justice League.