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.
One idea could be a time - traveling adventure. Batman Beyond gets sent back in time to the era of the original Justice League. He has to team up with them to stop a threat that was once thought defeated but has returned in a new form. The contrast between the high - tech world of Batman Beyond and the more classic superhero settings of the original Justice League would create interesting dynamics.
One idea could be a story where Batman has to lead the Justice League in a fight against a powerful new villain who can manipulate time. This would put Batman's strategic skills to the ultimate test as he tries to coordinate the different powers of the League members. Another plot could be that a member of the Justice League is secretly under mind control and Batman has to figure out who it is before they cause too much damage.
One idea could be that Batman discovers a hidden agenda within the Justice League that he believes endangers the world, so he decides to oppose them. For example, he might find out that a new technology the League is using has unforeseen and dangerous side effects.
One idea could be a story where Batman has to lead the Justice League in a fight against a new, powerful and mysterious villain that can manipulate time. Another could be a fanfiction exploring the relationships within the Justice League when they are stranded on an uninhabited planet and have to rely on each other more than ever.
A possible plot idea is that Batman discovers a dark secret within the Justice League that they are unaware of. This secret could be something that could potentially destroy the League or change their moral compass. Batman then has to decide whether to confront the League directly or try to fix the problem on his own, which causes the 'vs' situation as the League may see his actions as a threat.
One idea could be exploring Batman's initial reaction to being part of the Justice League in a 'Batman Begins' context. Maybe he's hesitant at first, still haunted by his past traumas from 'Batman Begins' and having to learn to trust these super - powered beings. He could be constantly assessing the League's motives and methods, which could lead to some internal conflicts within the team.
One interesting plot could be Batman's distrust of the Justice League's unrestrained power leading to a full - on confrontation. He might secretly plan to take down each member one by one, using his intellect and prep time. Another could be the Justice League being mind - controlled and Batman having to fight them to break the control.
A cool concept could be a 'Batman Justice League fanfiction' set in an alternate universe where the League is formed much earlier in history. Batman has to adapt to working with heroes from different time periods and cultures, and they all have to figure out how to use their powers in a world that's not as technologically advanced as their own.
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.