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.
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 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.
The combination of two distinct universes makes it unique. Mystery Skulls has its own set of characters with their own powers and personalities, and Danny Phantom also has a rich world of ghosts and superpowers. When combined in fanfiction, it creates a whole new set of stories and interactions that you won't find in either of the original works.
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.
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.
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.
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.
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.
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.
A cool concept could be a possession story. A powerful supernatural entity tries to possess members of both groups. Scooby Doo and the Mystery Skulls have to find a way to stop it before it's too late. This would bring out different reactions from the characters. Scooby and Shaggy might be more panicked, while the Mystery Skulls, with their prior experience, would be more strategic in their approach.