You should also do some research on both Danny Phantom and Supernatural. Know the powers and personalities of the characters well. For Danny, understand his ghost powers and how he uses them. For Supernatural, know about the different monsters, the lore, and the way the Winchester brothers operate. After that, create an outline for your story. Decide on the beginning, middle, and end. Maybe start with a mystery or a problem that Danny and the Supernatural characters have to solve together.
There are fanfictions where Danny's ghost powers are somehow connected to the demon - hunting world of Supernatural. Maybe his powers are seen as a new type of supernatural ability that the hunters in Supernatural are trying to understand. Some fanfictions explore how Danny would react to the more gritty and dangerous world of Supernatural, and how he could use his unique abilities to survive and help.
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.
Well, in this kind of fanfiction, Danny could be controlled by an ectoplasmic parasite. The parasite latches onto Danny and takes over his actions. His eyes might glow a different color to show he's not in control. His friends would first be confused, then realize something is amiss and start investigating.
Another possibility is that he's facing some emotional turmoil. Danny has a lot on his plate. He has to keep his identity a secret from his friends and family, deal with school, and fight ghosts. All this stress could be causing him to lose his appetite. He might be too worried or preoccupied to even think about food.
One possible story could be that Danny is facing a new and extremely powerful ghost. He needs help from his friends Tucker and Sam. Maybe they need to find a rare artifact to defeat this ghost. They could start by researching in the local library, looking through old ghost lore books. Tucker uses his tech skills to try and track down any leads on the artifact's location, while Sam uses her knowledge of the occult.
One idea could be that Danny gets an illness that affects his ghost powers. For example, he might start losing control over his intangibility or invisibility. This could lead to some really comical or dangerous situations. Another idea is that his friends try to find a cure for his strange ghost - related illness while also keeping it a secret from the town.
One idea could be that Danny's ghost powers are mistaken for some sort of demonic or otherworldly power by the Winchesters. They might initially try to hunt him down, but then realize he's not a threat and they team up to fight a greater evil that is related to both the ghost world and the supernatural creatures they usually deal with.
Obviously, the main character would be Danny Phantom himself, but in two different forms or versions. One would be the original Danny Phantom from the canon source, and the other would be a version created by the fanfiction. There might also be his friends like Sam and Tucker who could play important roles in helping the two Dannys understand each other and deal with any issues that arise from their meeting.
He might meet a nurse who has some sort of psychic ability and can sense that Danny is different. This could lead to an interesting interaction where Danny has to be extra careful.