Perhaps there's a character from Danny Phantom's world who has a connection to someone in the Mystery Skulls' past. This connection is uncovered during an investigation into a series of strange disappearances. As they dig deeper, they find out that it was all part of a plan by an old enemy who wants revenge on both Danny and the Mystery Skulls. So they must combine their forces to face this common foe and protect their respective worlds.
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.
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.
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.
One idea could be that Danny's ghost powers start to malfunction in the TMNT's dimension, causing strange ghostly events that the turtles have to help him fix. Another could be a villain from Danny's world teams up with one of the TMNT's foes, forcing the two groups to work together. Maybe Danny accidentally gets sent to the sewers where the turtles live and they initially mistake him for a new type of mutant.
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.
Well, there could be a story where Danny's ghost sense starts acting up in the Naruto world. It turns out that there are some spirits there that are similar to the ghosts in his world. Naruto thinks Danny is crazy at first but then they discover that these spirits are tied to an ancient curse. Together, they have to find a way to break the curse. Danny uses his ability to communicate with ghosts to learn more about the spirits, and Naruto uses his determination and strength to face any physical challenges that come their way.
A possible plot is that a powerful ghost in Danny's world has a connection to an ancient demon in Inuyasha's world. This connection is causing chaos in both worlds. Danny and Inuyasha meet and initially are at odds because they don't trust each other. But as they start to learn about the threat they face together, they begin to work together. Danny uses his energy blasts and Inuyasha uses his Tessaiga to fight the combined forces of the ghost - demon entity.
Maybe Danny gets transported to a different dimension where there is a harem - like society. The local girls there are intrigued by his ghost powers and his heroic nature. They start following him around, and he has to figure out how to deal with their attention while also trying to find a way back home. Some of the girls might be from different species, which could add more interesting elements to the story, like different cultural norms regarding relationships.
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 a fanfic where Danny discovers a new power that has unexpected consequences. For example, he might gain the ability to time - travel and has to deal with the chaos it causes in the timeline. Another idea is a fanfic that focuses on Danny's relationships in the ghost zone. Maybe he forms an alliance with a powerful but misunderstood ghost. A third idea could be a story where Danny has to go undercover as a human in a place full of ghosts who don't know he's half - ghost.
One idea could be that Danny Fenton and the Mystery Twins, Dipper and Mabel, cross paths while investigating a supernatural mystery that involves both the Ghost Zone from Danny Phantom and the strange anomalies in Gravity Falls. Maybe a powerful ghost has escaped into Gravity Falls and is causing chaos there, and Danny has to team up with the twins to stop it.