Another storyline might involve Danny being wrongly accused by the Justice League of a crime he didn't commit. As he tries to prove his innocence, he uncovers a deeper conspiracy that threatens both the human world and the Ghost Zone. He has to use his wits and powers to clear his name and save the day.
A great storyline could also be Danny Phantom teaching some of the Justice League members about the nature of the Ghost Zone. For example, he could help Flash understand how time works differently in the Ghost Zone, which could come in handy during a mission where they need to manipulate time to stop an enemy.
One interesting crossover could be Danny using his ghost powers to help the Justice League in a fight against a supernatural threat that they can't handle with their usual powers. For example, if there's a villain who can manipulate dark energy in a way that affects the living but not the dead like Danny. Another could be Danny's friends from his world interacting with the sidekicks in the Justice League universe, leading to some comical and heartwarming moments as they compare their different experiences.
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.
I'm not entirely sure as I haven't read this specific fanfiction. It could be about a disrupted or alternative version of a story where Danny Phantom interacts with the Justice League in some unexpected or 'broken' way.
One common theme is the clash of two different worlds. Danny comes from a world where ghosts are a big part of his life, and the Justice League is from a more traditional superhero world. So there's often a theme of how they deal with each other's differences.
One interesting storyline could be Paulina finally realizing Danny Phantom and Danny Fenton are the same person. She could initially be shocked but then come to accept it and they team up to fight a new powerful ghost. It would add a whole new dynamic to their relationship.
A third interesting storyline might involve a secret alliance between a member of the Justice League and a villain that the Young Justice team discovers. This discovery then sets off a chain of events where the Young Justice team has to decide whether to trust the rest of the Justice League and how to handle this new information without causing a complete breakdown in the superhero community.
Danny could use his ghostly powers to disrupt the technology that some Justice League members rely on. For example, he could mess with Cyborg's systems. His ability to overshadow people might also be a key factor, allowing him to control some of the less - powerful members.
In this fanfiction, perhaps Danny Phantom discovers a plot against the Justice League early on. He then uses his invisibility and intangibility to gather information. His ability to fly and super strength (in his ghost form) would be crucial in battles against the villains targeting the League. For example, if the villains had some sort of kryptonite - like weapon against Superman, Danny could use his powers to either disable the weapon or protect Superman until they find a way to neutralize it.
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.
In such a crossover, Danny could team up with Superman. Danny's ghost powers would be really interesting combined with Superman's super strength. Maybe they'd fight a common enemy that has powers related to both the supernatural and advanced technology.