One idea is that the Akatsuki from Naruto are after some powerful artifact in the Young Justice universe. Naruto and his friends follow them through the rift. Once there, they meet the Young Justice team. The two groups have to learn to communicate and understand each other's strengths and weaknesses. Naruto's sage mode could be a huge asset in battles against powerful foes in the Young Justice world. And the Young Justice members could introduce Naruto to concepts like teamwork in a different context than he's used to in Konoha.
Well, it could start with a rift opening between the two universes. Konoha ninjas pour into the Young Justice world. The Young Justice members would be intrigued by their ninja skills. The crossover might also focus on the differences in their fighting styles. Naruto's clones could be a real head - turner for the Young Justice crew. And perhaps they would team up to fight a common enemy that somehow threatens both universes, like an evil organization that wants to harness both chakra and meta - human powers.
A possible plot could involve Naruto characters being transported to the Young Justice universe. For example, Naruto himself could end up in Mount Justice. His unique abilities like the Rasengan would shock the Young Justice team. They might initially be suspicious of him, but as they see his determination to protect, they could start to work together. Maybe Naruto would learn about the different powers and technology in the Young Justice world, and in turn, teach them about chakra.
One possible plot could be that the Young Justice team somehow gets transported to the Naruto universe. They could team up with Naruto and his friends to fight a common enemy like Orochimaru, who has somehow managed to get his hands on some advanced Young Justice tech. This would create an interesting dynamic as the two groups learn from each other's fighting styles and powers.
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 interesting plot could be that the Young Justice team gets accidentally transported to the Avengers' universe. They initially face misunderstandings as the Avengers are suspicious of these new, young heroes. But then they realize they have a common enemy. For example, a powerful villain is trying to take over both universes. So, they must combine their skills and resources to stop the villain. The Young Justice members' unique powers and the Avengers' experience would make for a great dynamic.
Well, a possible plot could involve Naruto's world of ninjas colliding with the supernatural realm of Nurarihyon no Mago. Maybe Naruto and his friends are on a mission and accidentally cross into the other world. There, they could meet Rikuo and his yokai friends. They might initially be at odds due to differences in their powers and cultures, but then realize they have a common enemy. Together, they could fight against some dark force that threatens both their worlds.
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.
Some characters like Superboy might be a bit jealous of Naruto's natural charisma and the way he can easily make friends. But as they face challenges together, they would start to respect each other. Naruto would be fascinated by Superboy's strength. The more magical characters in Young Justice might be interested in how chakra is related to magic in Naruto's world. And Naruto would be eager to learn about their magic. There could be a lot of cultural exchange between the two groups, which would lead to some really interesting character interactions.
A possible interesting plot could be that a powerful artifact from Naruto's world ends up in the Young Justice universe. Naruto follows it and meets Cheshire. Cheshire, seeing an opportunity for herself, decides to team up with Naruto to find the artifact. Along the way, they face various foes and obstacles. Naruto's positive attitude starts to rub off on Cheshire, and she begins to question her own motives and actions.
Well, in such a fanfiction, there could be a situation where the Justice League is facing a threat that they can't handle alone. So they seek help from the Naruto universe. The Uchiha clan's powerful jutsu could be a great asset. Sasuke, for instance, could use his Chidori in combination with the Flash's speed. It would be a battle of different powers and strategies. Also, Wonder Woman might find similarities between her Amazonian values and the values of the shinobi in Naruto's world.
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.
Robin's intellect and strategic thinking along with Shikamaru's own intelligence would be quite something. They could plan elaborate battle strategies. Robin could use his knowledge of technology and gadgets to set up traps, and Shikamaru could use his understanding of the terrain and ninja tactics. Together, they could outwit even the most cunning of enemies. Also, Aqualad's water - based powers could be enhanced by the water - related jutsu in the Naruto world. He could learn new ways to manipulate water from the water - style ninja.