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.
Perhaps the Joker manipulates Batman into believing the Justice League has turned evil. He could plant false evidence or use mind - control on some of the League's members to make them act erratically. Batman, being the detective he is, starts investigating and ultimately ends up in a conflict with the League.
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 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 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.
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 misunderstanding that leads to a battle. Maybe a villain manipulates the situation so that Young Justice thinks the Justice League has turned evil. For example, the villain uses mind - control technology on some of the League members and Young Justice has to fight to save them.
One idea could be a misunderstanding that leads to a fight. Maybe the Justice League mistakes some of Young Justice's actions as being too reckless and end up in a battle. Then they realize they were wrong when a real threat emerges and they have to work together.
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.
Well, a cool plot could be time - travel related. Say a device sends members of the Avengers back in time to the DC universe and they accidentally disrupt something that makes the Justice League think they're invaders. Or perhaps there's a villain who has the power to manipulate minds on a large scale and he turns the two teams against each other. Also, a plot where the two teams have to compete in a series of challenges set by an ancient being for some great reward, but the challenges are designed to make them fight each other.
One idea could be that a powerful cosmic entity forces them to fight. It creates an artificial situation where they believe the other group is a threat to the universe. For example, it manipulates their perceptions so the Avengers think the Justice League is stealing powerful artifacts to control the multiverse, and vice versa.
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.