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.
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.
One idea could be that the Outsiders are called in to help the Young Justice team when a new, powerful and mysterious villain emerges. This villain has a unique power that neither team has faced before, forcing them to combine their skills and resources.
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.
One idea could be that the two teams are forced to compete in a series of challenges by a mysterious villain. This would lead to some friendly rivalries and also force them to learn from each other's strengths. For example, the Teen Titans' experience with magic-based threats could help the Young Justice team, while Young Justice's strategic planning might be beneficial to the Titans.
One idea could be that Ghost Rider's powers are somehow needed to stop a demonic threat in the Young Justice universe. Maybe a powerful demon is causing chaos and the team realizes they need the unique abilities of Ghost Rider to send it back to hell. Another plot could involve a member of Young Justice being possessed and Ghost Rider having to help exorcise the demon while also teaching the team about the darker, supernatural side of their world.
One idea could be that Naruto is somehow transported to the Young Justice universe. He then has to learn how to work with the team while also dealing with villains he's never faced before. Another plot could be that a villain uses some sort of magic or technology to merge the two worlds, forcing Naruto and the Young Justice members to cooperate to separate them again.
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.
One idea could be that Batman has to train the Young Justice team in a special stealth mission. He could teach them his unique detective skills and how to use the shadows to their advantage. For example, Robin could learn some new moves directly from Batman in this crossover.
One idea could be that the Avengers end up in the Young Justice universe due to a malfunctioning portal. They team up with the Young Justice team to fight a common enemy, like a powerful alien threat that neither group could handle alone. The characters' different skills and personalities would create great interactions.
One idea could be a crossover where the Young Justice team has to team up with the Justice League to face an interdimensional threat. Maybe a powerful villain from another dimension is trying to invade Earth and the combined skills and powers of both groups are needed to stop it.