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.
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.
One idea could be that an ancient, powerful enemy emerges that the Justice League alone can't handle. Supergirl, with her unique Kryptonian powers and different perspective, joins them. She might introduce some Kryptonian technology or fighting techniques that give them an edge. For example, she could have a device that can neutralize the enemy's energy - based attacks.
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.
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 a new villain emerges who has the ability to manipulate time, which affects both Young Justice's world and Central City where The Flash operates. The heroes from both groups have to work together to stop the villain before time is completely disrupted.
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.
A crossover with the Avengers. Picture the Justice League and the Avengers having to work together to stop an interdimensional threat. There would be clashes in leadership styles between Captain America and Superman, and also a lot of cool moments as different power - sets are combined to fight the enemy.
One exciting plot could be that Thanos teams up with Darkseid. The Avengers and Justice League initially misunderstand each other's motives while trying to stop this powerful alliance. They end up in battles among themselves until they realize they need to work together. Iron Man and Batman could be the first to figure it out, using their intellects to analyze the situation.