The Court of Owls would be a great main villain. They are a powerful and secretive organization in Gotham. Their connection to Gotham's history and their shadowy nature could pose a huge threat to both Young Justice and Batgirl. They might be after some meta - human power or trying to take over Gotham in a new way.
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.
The plot might center around a mystery that ties to both Young Justice's world and Batgirl's. For instance, some sort of ancient artifact that has the power to disrupt both the meta - human world and Gotham's criminal underworld. Young Justice brings their diverse powers and abilities, while Batgirl offers her detective skills and knowledge of Gotham. As they search for the artifact, they face various challenges and enemies.
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.
Vandal Savage could be a great main villain. Since he has a long - standing history in the Young Justice universe, he could be using the chaos of Endgame to his advantage. He might be secretly manipulating events behind the scenes to further his own goals of world domination.
Vandal Savage is also a possibility. He has a long - standing enmity with the heroes. Maybe he has a new plan that involves using the resurrected heroes for his own evil purposes, or he's trying to stop their resurrection because he fears they'll thwart his future 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.
Well, it might involve Batgirl initially being a bit of an outsider among the Justice League. But then she proves her worth by taking on a powerful villain that the League has trouble with. For example, she could use her agility and stealth to infiltrate the villain's lair and gather crucial intel that the League needs to make their big move.
Well, there's a writer named 'NightWingFan23' who has written some really engaging Young Justice Batgirl fanfics. Their stories often focus on Batgirl's growth within the Young Justice setting.
She is a key player. Her role can be as a strategist, using her sharp mind to plan missions. Just like in the official DC universe, she can analyze situations quickly.
Maybe Batgirl is sent by Batman to assist Young Justice on a mission. She has to adapt to their more light - hearted and less brooding approach compared to the Bat - family. Along the way, she forms a special bond with a particular member of Young Justice, perhaps Artemis. They have to overcome their differences, like Batgirl's strict no - killing rule and Young Justice's sometimes more lenient attitude towards villains, in order to succeed.