One idea could be to have Ben Tennyson end up in the Young Justice universe by accident. Maybe his Omnitrix malfunctions during a fight and transports him there. He could then team up with the Young Justice heroes to fight a common enemy like the Light or some new villain that's a threat to both universes.
In a Young Justice and Justice League crossover fanfiction, character development can occur in multiple ways. Firstly, the less - experienced Young Justice members can learn from the Justice League's vast knowledge and experience. A character like Robin in Young Justice could gain new insights into detective work from Batman. On the other hand, the Justice League members can be inspired by the Young Justice team's energy and fresh perspectives. Superman might see the determination of a young hero like Superboy and start to reevaluate his own approach to heroism. Also, characters can develop through shared traumas. If they face a particularly difficult villain who causes a lot of destruction, they might all grow in their empathy and understanding of the importance of protecting civilians.
Another theme is the exploration of new powers and abilities. When they cross over into different universes or teams, characters often have to adapt to new powers or face enemies with unfamiliar abilities. It makes for some really interesting storylines. For instance, if a Young Justice character crosses over to a magical - based universe, they might have to figure out how to deal with magic for the first time.
One idea could be that Naruto is somehow transported to the Young Justice universe and his chakra is mistaken for a form of magic. This could lead to some interesting team - ups and misunderstandings as the Young Justice characters try to figure out who Naruto is and what his 'magic' can do.
A fanfiction about Naruto and Batgirl in the Young Justice setting could explore different themes. It could be about cultural exchange, as Naruto comes from a very different world than the DC universe. Their combined efforts could also be centered around protecting the innocent. Maybe they have to stop a powerful villain who is threatening both the ninja world Naruto comes from and the Young Justice world. Their different abilities would be crucial in this fight, with Naruto using his Rasengan and Batgirl using her Batarangs and martial arts skills.
Naruto would be a bit of a wild card at first. His brash and head - strong nature might clash with some of the more reserved members of the Young Justice team, like Aqualad. But his determination and loyalty would also be something that the team could quickly come to respect. He would probably befriend Superboy quickly as they both have a bit of an outsider feel.
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.
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.
The experienced members of the Justice League would likely take on a mentoring role. For example, Superman might offer advice to Superboy on how to better control his powers. Batman would probably be more cautious about involving the Young Justice team in dangerous missions, while the younger heroes would be eager to prove themselves. Aqualad could learn new underwater combat techniques from Aquaman. This would create a dynamic of growth and learning between the two groups.
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.