One idea could be Naruto being transported to the Young Justice universe during the Invasion arc. He could use his unique jutsu skills like the Rasengan to fight off the invaders. Maybe he teams up with the Young Justice team and teaches them some of his ninja techniques.
The idea of Superboy's powers evolving or him learning to control them better is also quite common. In many fanfictions, he has to face new challenges that force him to push the limits of his abilities. Also, there are often themes related to loyalty and betrayal. Given the nature of the Young Justice Invasion story, there can be situations where Superboy has to decide who to trust.
A great plot for Young Justice Invasion fanfiction might be to have the team deal with internal conflicts during the invasion. Maybe there are trust issues among some members because of secrets that come to light. For example, if a member was unknowingly related to one of the invaders. This would create drama and force the team to work through their issues while also fighting the external threat. Also, you could explore how the invasion affects the public perception of the young heroes. Are they seen as saviors or are people scared of them bringing more danger?
In this type of fanfiction, magic could play a role in character development. For Naruto, experiencing a different type of power system like magic in the Young Justice world could make him question his own ninja way. He might start to adapt some of the magic concepts into his own fighting style. And for the Young Justice characters, learning about Naruto's 'magic' (chakra) could open their eyes to new ways of thinking about power and how to use it more effectively.
Artemis is a character that could be explored more in fanfiction. She has a complex backstory and during the Invasion, she could be given more depth. For example, her relationships with other team members could be further developed, especially how she deals with the stress and danger of the invasion while also maintaining her cover if she still has one at that point.
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 possibility could be that Naruto's anti - hero status in the Young Justice fanfic is due to him being a loner. Maybe he doesn't trust the Young Justice team at first because of his past experiences. He might have his own way of doing things that doesn't always align with the team's methods, like being more brutal in combat against villains.
Another option is to follow some Young Justice fanfiction writers on social media platforms like Twitter or Tumblr. They might promote their own works or share other great fanfictions they've come across. Some of them focus specifically on Superboy in the context of Young Justice Invasion, and you can get direct access to their creations this way.
In a Young Justice fanfiction, Naruto's Sage Mode could change the power dynamics significantly. His Sage Mode gives him access to nature energy, which could interact in strange ways with the various powers and technologies in the Young Justice world. For example, his ability to blend into nature while in Sage Mode might make him an excellent spy or infiltrator. Plus, his battle experience and strategic thinking from the Naruto world could help the Young Justice team in their missions.