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 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.
In a fanfiction, the Ghost Rider could form an alliance with Batman. Batman would be intrigued by the supernatural element that Ghost Rider brings. They could team up to take on villains who are using magic or other dark forces. Ghost Rider's powers of hellfire and his unearthly strength would be a great asset to the Dark Knight's strategic mind.
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.
A possible plot is that the Ghost Rider's hellfire has an unexpected effect on the vampires in Twilight. Since vampires are undead, the hellfire might either have no effect, or it could be the one thing that can truly destroy them. This could lead to a race between the vampires and the werewolves to either use or stop the Ghost Rider. Also, the Ghost Rider could form an alliance with the werewolves as they are more in tune with the natural order which the Ghost Rider also represents in a way.
A crossover with Kamen Rider Zi - O could also be really cool. Zi - O travels through time, so he could accidentally disrupt the timeline in a way that affects Ghost's world. Ghost might have to team up with Zi - O to fix the timeline while also dealing with the enemies that are taking advantage of the time - chaos. They could encounter different versions of themselves from alternate timelines and have to figure out how to make things right.
Maybe the Ghost Rider's powers are somehow connected to an ancient magic in Equestria. He could be on a quest to find out the origin of his powers and in the process, he befriends Rainbow Dash. Rainbow Dash is intrigued by his ability to fly on his flaming motorcycle and they start to explore different parts of Equestria together, all while uncovering secrets about his powers.
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 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 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.