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.
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.
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.
One idea could be that the Totally Spies are sent on a mission to investigate some strange paranormal activities. They then discover Danny Phantom's world and team up with him to stop an evil force that is using both magic and technology to take over the world. Danny could teach them about the Ghost Zone and they could share their spy skills with Danny.
I like the idea of a Danny Phantom and Ben 10 crossover. Ben has the Omnitrix which gives him access to different alien forms, and Danny has his ghost powers. They could either be rivals at first, each thinking their powers are better, or they could quickly team up to face a threat that requires both their unique abilities. It would be a fun clash of two very different power - based universes.
One interesting fanfic concept is that Danny and Ember are forced to work together to save the Ghost Zone from a powerful, ancient evil. They must combine their powers and knowledge. Danny's scientific knowledge about the Ghost Zone and his powers, along with Ember's knowledge of the more mysterious and musical aspects of the Ghost Zone, could lead to a great adventure and a deepening of their relationship.
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.
One idea could be that Danny and the Winchester brothers team up to fight a ghost that is causing chaos in both the Ghost Zone and the human world. Maybe it's a powerful entity that has the ability to cross between dimensions easily.
Another idea is a crossover with a superhero universe. Imagine Danny Phantom's Ghostly Wail being used in a fight against some supervillains. He could cross paths with a young superhero who is initially scared of Danny because of his ghostly appearance. But when they see how Danny uses his powers, especially the Ghostly Wail, for good, they team up. Danny could teach the superhero about the ghostly realm and how to deal with supernatural threats.
One idea could be that Danny's ghost powers somehow interact with the Cybertronian technology in the Transformers Prime universe. Maybe his ectoplasmic energy can power up or disrupt certain Cybertronian devices. For example, he could accidentally short - circuit a Decepticon weapon while trying to use his powers to protect a human from an attack.
A plot could revolve around a new villain who has the power to manipulate both ghosts and the strange artifacts that the Mystery Skulls often deal with. Danny, with his ghost powers, and the Mystery Skulls, with their unique skills and knowledge, have to team up to stop this villain from achieving their evil goals. For example, the villain could be trying to open a portal that would merge the Ghost Zone with the Mystery Skulls' dimension in a catastrophic way.