Perhaps a new villain that was created as a result of some future technology gone wrong. This villain could be targeting Future Robin specifically because he's trying to stop their plans. And in the Young Justice world, they start causing chaos to draw him out. The team would have to figure out how to fight this new and unknown threat with the help of Future Robin.
It could be a future version of an existing villain who has somehow gained even more power. For example, a more advanced and menacing version of the Light. They might be the ones causing the future problems that Future Robin is trying to prevent, and their actions in the present are just the start of their grand plan.
Well, it might involve a clash of ideologies. Young Justice has their own way of doing things, and Future Robin, having experienced more, could have a different approach. This could lead to some interesting conflicts within the team as they try to figure out how to incorporate his ideas while still staying true to their own values. There could also be a mystery that only Future Robin knows about, and he has to convince the Young Justice team to help him solve it.
One idea for this fanfiction could be that Robin is mind - controlled by a powerful villain. The villain uses Robin's skills and knowledge of the Young Justice team to plan elaborate attacks. Robin, under the control, starts to act in ways that are completely against his usual heroic nature, causing chaos within the team as they struggle to understand what has happened to him.
A possible plot is that Robin has a falling out with the Young Justice leadership. He feels that their methods are too soft or that they are not making a real difference. Frustrated, he decides to join the villains who promise him a more 'direct' approach to dealing with the world's problems. He could then be involved in high - stakes heists and battles against his old comrades, all while grappling with his new identity as a villain.
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.
New recruits from different parts of the world could also be main characters. Maybe a young hero from Africa with the power to control plants, who brings a whole new perspective to the team. They would have to learn how to work with the more established heroes in Young Justice.
A new, original character could be created as the antagonist. Maybe a powerful and vengeful assassin who has a grudge against Robin for some past event. This character could have unique abilities and a personal vendetta that drives the conflict in the fanfiction.
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.
Obviously, the main character would be the one who would become Robin. But there could also be other important characters like his trainers or guardians. For example, an old martial arts master who taught him the ways of combat.
A new super - villain group that wants to take over the world might be behind it. They figure that by experimenting on Robin, they can learn the secrets of the Young Justice and use that knowledge against them. Or perhaps an old enemy of Batman who wants to get back at him by harming his protege.
Lex Luthor could be a great villain. He's always interested in taking down the Justice League and its affiliates. He might see the clone as a way to disrupt the Young Justice team and gain an advantage over Wonder Woman.