One possible plot is that Danny gets accidentally transported to the Young Justice universe. At first, the team is suspicious of him, but as they see him fight against some common enemies, they start to trust him. Danny then has to learn to work within the team's dynamics while also dealing with his own personal issues from his home universe.
Well, it could be about Danny's powers being a great asset to the Young Justice team. Maybe he helps them with his ghostly abilities like intangibility and invisibility during a mission where they need to infiltrate a highly - guarded enemy base. His unique perspective as a half - ghost could also offer new strategies to the team.
One possible plot could be that Danny Phantom's ghostly abilities are detected by the Justice League. They initially view him as a threat but then realize he can be an asset. Danny could help them with foes that have intangible or otherworldly powers. For example, against an enemy that can phase through walls or possess people, Danny's experience dealing with ghosts would come in handy.
The plot might involve Danny Phantom being mistaken for a meta - human in the Young Justice world. At first, there could be some distrust from the Young Justice members, but as they get to know him and his powers, they realize he can be a great asset. They could end up on a mission to stop a powerful ghost - like being that has invaded their dimension. Danny would use his knowledge of the ghost zone to help them understand this new threat and together they'd come up with a plan to defeat it.
Well, he could bring his unique ghost powers to the team. His intangibility and invisibility would be great for stealth missions. And his ghost ray could be a powerful offensive weapon. Maybe he'd also have some funny interactions with the more serious Justice League members like Batman.
One interesting plot could be that a powerful ghostly villain from Danny's world somehow crosses over into the Young Justice universe. This villain starts causing chaos and Danny has to team up with the Young Justice heroes to stop it. Along the way, they learn about each other's powers and worlds.
It could be a powerful ghost that has somehow made its way into the Young Justice universe. This ghost might be after some powerful artifact that exists in the Young Justice world and Danny and the team have to stop it.
Maybe there's a villain who has the ability to cross between the dimensions of Danny's world and the Young Justice world. Danny and the Young Justice team have to combine their efforts to stop this villain. Danny could teach them about dealing with supernatural threats, while they could show him how to work better in a team setting in a more traditional superhero sense.
I think it could be Superman. Superman is all about truth and justice and he would likely see the good in Danny. Also, they both have super strength in a way. Danny has his ghostly strength and Superman has his Kryptonian strength. They could bond over protecting the innocent.
One possible plot could be that Danny Phantom is facing a threat in his own dimension that is beyond his control. He decides to call the Justice League for help. Maybe he first has to figure out a way to contact them across dimensions. Once he does, the Justice League initially doubts his claims but as they start to investigate, they realize the severity of the situation and they all work together to fight the new and strange enemies from Danny's world.
If Naruto joins Young Justice in fanfiction, he might introduce the concept of chakra to the team. This could open up new ways for them to develop their powers or enhance their existing abilities. He could also form interesting relationships with the characters. For example, his friendship with Robin could be based on their shared leadership qualities and intelligence. And his combat skills would make him a valuable asset in taking on powerful villains.
One possible plot could be Nightwing joining Young Justice as a mentor. He'd bring his years of experience from being Robin and working with Batman. He could train the young heroes in new combat techniques and also teach them about stealth and detective work.