One idea could be that Batman Beyond travels back to the time of the original Batman and has to team up with him to stop a villain who has also time - traveled and is trying to change history for his own evil gains.
Maybe Batman Beyond could accidentally get sent to a future even further ahead than his own time. There, he discovers a new threat that is related to a past event in the Batman Beyond timeline. He then has to figure out how to use his knowledge of both past and his own time to stop it. For example, the new threat could be a technology that was misused in the past and has now evolved into a much greater danger.
One idea could be that Batman Beyond travels back to the time of the original Batman and has to team up with him to stop a villain who has also time - traveled. They would have to combine their different skills and technology from their respective eras.
One idea could be Batman traveling back to the time when Gotham was first founded. He could try to prevent the seeds of corruption from being sown. Another plot could be him traveling to a future Gotham that has been completely overrun by villains and he has to find a way to change that future by altering events in the past. Or perhaps he travels to different time periods to gather knowledge and technology to better fight crime in his own time.
One idea could be exploring Robin's struggle to live up to Batman's legacy in the Batman Beyond era. Maybe he has to face a new villain who is specifically targeting the new Batman and Robin duo because of their connection to the old heroes. Another plot could involve Robin discovering a long - lost technology from the original Batman's days that holds the key to stopping a major threat to the future Gotham.
One idea could be exploring Inque's past before she became a villain. Maybe she was an ordinary person who got caught in some scientific experiment gone wrong. Another plot could involve a team - up between Batman Beyond and Inque against a greater threat that endangers the whole city. They could start off as reluctant allies but gradually learn to trust each other.
A cool plot could be that there is a rift in the multiverse that is causing chaos. Batman Beyond discovers it first and tries to get the Justice League's help. Along the way, they encounter alternate versions of themselves and have to work together to close the rift while also dealing with the differences and similarities between their various selves.
Perhaps they could start off as rivals in the fanfiction. Batman from the present is skeptical of Batman Beyond's more high - tech approach. But as the story progresses, they learn from each other and become a great team. For example, Batman could teach Batman Beyond some of his old - school detective skills, while Batman Beyond shows Batman new ways to use technology in combat and surveillance.
Another plot could involve traveling to a dimension where the villains have won. Batman Beyond has to team up with the few remaining heroes in that dimension to turn the tide. He might face versions of his own villains that are far more powerful and ruthless than he's used to. This would test his skills and his will to fight in a whole new way.
One idea could be exploring an alternate universe where Terry McGinnis (Batman Beyond) is pulled into the Injustice universe and has to deal with the morally compromised heroes. He might try to find a way to bring back the true sense of justice among them. For example, he could start by trying to reason with Superman, showing him the error of his ways through his own experiences in his own universe.
Another plot could involve a character from the original Cadmus in the Batman Beyond timeline. For example, a revived clone or an old scientist who has new plans. They could be using the advanced technology of the future to bring back old threats or create new ones. Batman Beyond would have to use his unique skills and gadgets to deal with this. He might also team up with some of the new heroes in the future Gotham to take on Cadmus.
A great plot could involve Nightwing training a new generation of heroes in the 'Batman Beyond' universe. He could share his old - school combat techniques with the more tech - reliant heroes, leading to some interesting clashes and growth. For example, he might have a hard time getting used to the new gadgets while the younger heroes struggle with his more hands - on combat style. And together they have to face a villain who is exploiting their differences.