There could be a conflict within the crossover fanfic where the technology of the Ghost Hunt team malfunctions because of the presence of Danny's unique half - ghost energy. This causes chaos as the team blames Danny at first. But they soon realize that they need to find a way to make their technology work in harmony with Danny's powers in order to defeat a group of ghosts that are causing havoc in the city.
For the crossover, a good plot could be that a new type of ghost appears that is immune to Danny's ghostly powers. The Ghost Hunt team, which has encountered a similar situation before, offers their expertise. They introduce Danny to a special type of ectoplasm - based weapon that can harm this new ghost. Danny then teaches them some of his combat moves as a half - ghost to better fight the ghost.
Another theme is power struggle. Danny has his own set of powers, but when interacting with other ghosts, there can be a battle for dominance or control. This adds a lot of action and drama to the fanfics.
A possible main antagonist could be a human who has somehow gained the ability to control ghosts and has made a deal with some dark force from the Mystery Skulls' world. This person wants to use the chaos of a crossover between the two universes to take over both the human world and the dimension where the Mystery Skulls operate. They would be a formidable foe as they can use both ghostly minions and the knowledge of the dark secrets from the Mystery Skulls' side.
In a Danny Phantom and Justice League crossover fanfic, Danny could team up with Superman. Maybe Danny uses his ghost powers to help Superman when he's facing a powerful ghost - like enemy that the Justice League can't handle with their normal tactics. It would be a really cool combination of the two universes.
One idea could be that Danny, as a half - ghost, has to prove himself to the Ghost King. Maybe there's a tournament in the Ghost Zone where Danny enters to show his worth. This could lead to some epic battles and alliances with other ghosts.
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.
One common theme is friendship. The stories might explore how Danny forms friendships with female ghost characters and how they support each other in the ghostly world.
One idea could be that Danny, with his ghost powers, ends up in the RWBY universe. He could team up with Team RWBY to fight off Grimm that are being influenced by some sort of ghostly energy. His intangibility and flight would be really useful in battles.
Perhaps an organization made up of both Pokemon world villains and some of Danny's foes. They could be working together to create a portal that would merge the two worlds in a way that benefits them. They would be the main antagonists as they cause all kinds of chaos, stealing both Pokemon and technology from both worlds to achieve their goals.
The main antagonist could be one of the powerful and malevolent entities from 'The Suffering'. For example, the big bad demon or the tortured soul that has been corrupted by the darkness of that world and now wants to spread it to Danny's world.