Well, it could be a story where the girl from the Pokemon world somehow gets transported to the Danny Phantom universe. Maybe she teams up with Danny to fight some common enemies that are causing chaos in both their worlds.
In a fanfic, it might be that the Danny Phantom character visits the Pokemon world and meets this girl. They could go on a journey together to discover some rare Pokemon while Danny also uses his ghost powers to protect the Pokemon and the girl from any threats.
It could be that there's a shared villain. A powerful entity that is causing problems in both the Pokemon world and the Danny Phantom world. The girl and Danny join forces to take on this villain. They combine their unique abilities, like the girl's Pokemon training skills and Danny's ghost powers to fight the bad guy.
Maybe in this crossover, some Pokemon are accidentally sent to Danny's world. Danny has to protect the Pokemon from being captured by the Guys in White while also trying to find a way to send them back. Meanwhile, a certain Pokemon, like Gengar, forms a special bond with Danny because of their shared ghostly nature.
One possible plot could be that Danny Phantom, while exploring some sort of interdimensional rift, gets zapped by a strange energy that transforms him into a Pokemon. Maybe he becomes a Pikachu. He then has to figure out how to use his new Pokemon abilities to get back to his normal form. He might start by trying to communicate with other Pokemon, learning their ways and using his ghostly knowledge to his advantage in the Pokemon world.
Perhaps there could be a love interest that is unique to his female form. Maybe someone who didn't notice Danny before as a boy, but now is attracted to him as a girl. This could add a whole new layer of drama and romance to the fanfiction, as Danny has to figure out how to handle this new relationship while still dealing with his ghost - hunting duties.
In this fanfiction, it could be that Danny Phantom meets a Danny Phantom from a parallel fan - made story. At first, they don't trust each other. But as they learn more about each other's worlds, they realize that there are some common elements that are being threatened. It could be that a powerful ghost is trying to rewrite all the fanfic universes related to Danny Phantom. So, they must combine their strengths and knowledge to stop this from happening.
In the 'Danny Phantom in the Civil War' fanfic, perhaps Danny is somehow transported to the time of the Civil War. He could find himself in a moral dilemma. On one hand, he wants to stop the bloodshed, but on the other, he doesn't want to interfere too much with history. He might end up using his powers in a more subtle way, like using his ecto - energy to heal the wounded without being noticed.
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.
There could be a fanfic where Danny and Ember accidentally swap powers. This leads to a series of comical and also dangerous situations. Danny has to figure out how to control Ember's power of influencing people through music while Ember struggles with Danny's more combat - oriented powers. It could be a story full of self - discovery for both of them.
In a Danny Phantom trans girl fanfiction, Danny could discover her true identity as a trans girl after an encounter with a special ghost. This ghost could be like a spirit guide that shows her visions of who she really is. Danny then has to figure out how to balance her newfound identity with her ghost - fighting duties. She may also have to deal with the reactions of her family, especially her parents who might be initially confused but eventually come around.
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.