One idea could be that Ghost Rider somehow gets transported into the Young Justice universe. He might initially be seen as a threat by the team. But then they realize he's fighting against a common evil that has ties to the dark forces in both their worlds. For example, a demon that is trying to open a portal to bring more chaos.
One idea could be a crossover where Ghost Rider teams up with the Young Justice team to fight a powerful demonic threat that neither could handle alone. Maybe they have to enter the underworld to stop a demon lord from opening a portal to Earth. Another idea is a story where a member of Young Justice is somehow cursed and starts to transform into a Ghost Rider - like figure, and they have to learn to control this new power while still being part of the team.
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 the Ghost Girl is actually a lost hero from another dimension. She has special powers that she doesn't fully understand and the Young Justice team has to help her control them while also trying to figure out how to send her back home. Another plot could involve the Ghost Girl being a spirit who is tied to a mystery that the team needs to solve. Maybe she was a victim of an old, forgotten experiment and her presence is a clue to stopping a new threat related to that experiment.
One idea could be an OC with unique powers joining the Young Justice team. For example, an OC who can manipulate time in small increments. This would create interesting scenarios during battles and team strategizing.
One plot idea could be that Venom somehow gets transported to the Young Justice universe and forms an uneasy alliance with the team. Maybe at first they see Venom as a threat but then realize his power can be used against a greater common enemy.
A possible plot could be a time - travel related one. A character from the Regeneration world accidentally travels to the Young Justice timeline and messes up some key events. Now the Young Justice team, along with the help of some friendly Regeneration characters, have to fix the timeline while also dealing with the consequences of the changes that have already occurred.
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.
One idea could be that Ghost Rider somehow gets transported to the world of Fire Force. He could team up with the Fire Force members to fight against a new type of infernal that has powers related to the underworld. His Penance Stare might be used to expose the true nature of some of the more mysterious infernals or even some corrupt individuals within the Fire Force organization.
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.
Maybe a story where some of the younger members of the Young Justice team are frustrated with the Justice League's methods and decide to take on a mission on their own, but end up getting in over their heads and have to call in the League for help. This could lead to a lot of character development and some interesting dynamics between the two groups.