A fun plot could be a time - travel mishap. Supergirl gets sent back in time and accidentally changes something that affects the future of the Justice League. So the League has to team up with her to fix the timeline. During this, they discover new things about each other's powers and also about their own pasts that were previously unknown.
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.
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 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.
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 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.
Perhaps a major plot twist could be that the tailed beasts in Naruto are somehow connected to the Mother Boxes in the Justice League world. When the Mother Boxes start acting up, it's because the tailed beasts are influencing them. This would force the Justice League and Naruto's friends to work together to figure out how to stop the chaos. Another plot twist could be that the Justice League members are transported to the Naruto world and have to adapt to the ninja way of life, and in the process, they discover new powers within themselves. And finally, if Naruto was able to summon a Justice League member as a summon, like if he could summon Superman instead of a toad, that would be a wild and unexpected plot twist.
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.
A cool plot could be a race between The Flash and Gotenks. They both pride themselves on their speed, so it would be interesting to see how that pans out. Also, perhaps Vegeta could befriend Batman as they both have that brooding, serious personality. They could exchange combat and strategy tips. And what if the Dragon Radar was used by the Justice League to track down an energy source that was causing chaos in both universes?
One idea could be that the Covenant from Halo discovers Earth while the Justice League is busy dealing with a local threat. The League has to quickly adapt to this new alien threat that has far more advanced technology than most of their foes. They might have to team up with Master Chief, who is also on a mission to stop the Covenant's invasion plans.
Well, a cool plot could be that some sort of cosmic event has merged their universes in a strange way. Members of the Avengers start showing up in the Justice League's world and vice versa. Iron Man could team up with Batman to figure out how to reverse the situation while Thor and Superman have an epic showdown that ends in mutual respect. And then they all work together to fix the messed - up universes.
One idea could be that a powerful cosmic threat emerges that neither the Justice League nor the Avengers can handle alone. So they have to combine their forces. For example, Superman and Thor could team up to take on a super - strong enemy, using their strength and lightning powers respectively. Batman and Iron Man might start off butting heads as they both think they have the best strategies, but eventually work together to outwit the villain's high - tech defenses.