Well, one possible plot could be that Supergirl is somehow transported to the Young Justice universe. Maybe there's a dimensional rift caused by some villain's experiment. She then teams up with the Young Justice team to stop this villain from causing more chaos across different dimensions. They could learn from each other's skills and powers along the way.
The crossover could start with a Young Justice mission gone wrong. They accidentally open a portal to Supergirl's universe. Supergirl, being the hero she is, decides to help them get back home. Along the journey, they encounter various challenges. Some of the Young Justice members might be in awe of Supergirl's powers, while others might try to prove themselves to her. And they all have to figure out how to close the portal before more unwanted things come through from either universe.
One possible plot could be that Naruto, through some interdimensional rift, ends up in the Young Justice universe where he meets Supergirl. They could start off as strangers, but quickly realize they have a lot in common. For example, both have superpowers and a strong sense of justice. Naruto's ninja skills and Supergirl's Kryptonian powers could combine in interesting ways during battles against common enemies. They might also have to overcome cultural differences, as Naruto is from a feudal - like ninja world and Supergirl from a more advanced, alien - influenced society in the Young Justice world.
One possible plot could be that a common enemy, like a powerful interdimensional villain, forces the Young Justice team and the Avengers to team up. They start off distrustful of each other, with the Avengers seeing the Young Justice members as inexperienced kids and the Young Justice team thinking the Avengers are too rigid. But as they face the villain's various attacks, they gradually learn to work together. For example, Superboy could team up with the Hulk in brute - force battles, while Robin and Iron Man use their intelligence to figure out the villain's weaknesses.
Well, the plot could involve Ben Tennyson and the Young Justice team teaming up to fight a common enemy like Darkseid. Ben could use his various alien forms to complement the powers of the Young Justice members. For example, Heatblast could help Superboy when dealing with cold - based threats.
Supergirl's no - nonsense attitude towards fighting villains would be an interesting contrast to the more youthful and sometimes impulsive nature of the Young Justice team. Aqualad, as the leader, would have to figure out how to incorporate Supergirl into their mission plans. She might be used to taking charge in her own battles, but she would have to learn to work within the team structure of Young Justice. And the team would have to adjust to her presence. For example, her super - strength could accidentally cause damage during training sessions if she's not careful. But over time, they would all grow to respect and rely on each other.
One possible plot could be that Subaru from 'Re:Zero' somehow gets transported to the world of 'Young Justice'. He might initially be confused but then use his 'Return by Death' ability to his advantage. For example, he could help the Young Justice team in battles by being able to predict enemy moves after dying a few times. His unique perspective on life and death could also influence the team's moral decisions.
A cool plot could be that a dimensional rift opens up and pulls some of the Young Justice characters into the Ben 10 universe. They then have to find a way to get back home. Along the way, they meet Ben and join forces with him. Ben shows them around his world, and they help him deal with some local threats. For instance, Aqualad could use his water - based powers in conjunction with Ben's Four Arms in a fight against a group of robotic enemies that are causing chaos in a city near Bellwood.
One idea could be that Spiderman gets transported to the Young Justice universe. He teams up with the team to stop a common enemy like Vandal Savage, who has some new high - tech weaponry. Spiderman's unique abilities like web - slinging and his spider - sense would add a new dynamic to the team's combat strategies.
One possible plot could be that Naruto is somehow transported to the Young Justice universe. He teams up with the Young Justice team. Naruto's unique jutsu skills like the Rasengan could be used to fight the villains in the Young Justice world. Maybe they face a common enemy that requires both Naruto's ninja abilities and the superpowers of the Young Justice members to defeat.
A really interesting plot could be a time - traveling crossover. Supergirl goes back in time to the era of the original Avengers. She helps them in a battle that changes the course of history. In return, the Avengers help her find a way back to her own universe. During this time, she forms a special bond with Thor, as they both have superhuman strength and a connection to otherworldly powers.
Well, one possible plot could be that Supergirl accidentally lands in the Naruto universe. Naruto, being the curious and friendly ninja he is, approaches her. They initially have a misunderstanding due to their different worlds and powers, but then they realize they can learn from each other. Supergirl could teach Naruto about her advanced technology from her world, while Naruto could show Supergirl the unique chakra - based powers and the ninja way of life.