A plot could involve a new villain who manipulates the two groups into fighting each other. The villain uses mind - control or false information. As the battle rages, some of the members start to suspect something is off and eventually figure out the truth and join forces to defeat the real enemy. This could also lead to some great character development as the heroes learn to trust each other more.
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 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 crossover where the Young Justice team has to team up with the Justice League to face an interdimensional threat. Maybe a powerful villain from another dimension is trying to invade Earth and the combined skills and powers of both groups are needed to stop it.
Maybe a story where some of the younger members of the Young Justice team are frustrated with the Justice League's methods and decide to take on a mission on their own, but end up getting in over their heads and have to call in the League for help. This could lead to a lot of character development and some interesting dynamics between the two groups.
One idea could be that the Young Justice team gets accidentally transported to an alternate dimension where the Justice League has turned evil. The Young Justice members then have to figure out how to reverse the situation while also evading capture from their once - heroes. Another could be a time - travel plot where the Young Justice team travels back in time and teams up with the early days of the Justice League to stop a threat that was thought to be long gone but has resurfaced in their own time. A third idea is that a powerful new villain emerges who can only be defeated by a combined effort of the Young Justice and Justice League, but first they have to overcome their differences in fighting styles and leadership.
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.
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 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.
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 that the Young Justice team has to prove themselves to the Justice League during a major alien invasion. The League initially doubts their abilities but as the battle progresses, they see the unique skills and teamwork of the young heroes.
A cool plot could be a time - travel related crossover. The Young Justice team travels back in time and meets the younger versions of the Justice League members. They have to work together to stop a time - traveling villain from changing history in a way that would destroy the future. Or perhaps there's a magic - based crossover where a powerful sorcerer is causing chaos. The Justice League, which is more used to physical threats, has to team up with the Young Justice, some of whom have magic - related powers, to defeat the sorcerer.