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 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 more complex plot could be that there is a prophecy in both universes that foretells of a combined force from both Naruto's world and the Young Justice world being the only thing that can stop an upcoming great evil. This would lead to a series of events where characters from both sides have to learn to trust and work together. Naruto could bring his friends from Konoha, and together with the Young Justice team, they would train and strategize to face this ultimate threat.
The interaction between Naruto and Miss Martian would be quite interesting. Miss Martian has her telepathic and shape - shifting abilities. Naruto, on the other hand, has his chakra - based powers. Miss Martian could be intrigued by Naruto's chakra system and Naruto could be amazed by her mental powers. Also, Naruto and Beast Boy could have some fun interactions. Beast Boy can transform into different animals, and Naruto might find that really cool and they could come up with some unique battle strategies together.
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.
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.
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.
It could be really exciting. Picture Naruto's ninjutsu skills combined with the superpowers of the Justice League members. For example, Naruto's shadow clone jutsu could be used in a really creative way during a battle against a common enemy that the Justice League and Naruto face. Maybe he could create clones to confuse villains like Lex Luthor while Superman uses his heat vision to take them down.
Perhaps a story where a character from the Naruto universe, who has a connection to Amaterasu, travels to the Young Justice world. There, they meet a character who has a similar power but in a different form. They exchange knowledge about their powers and together develop a new technique that combines the elements of both their abilities. This new power could then be used to save both worlds from a common threat.