One common theme is the clash of different worlds. The Scooby Doo gang is used to more 'family - friendly' mysteries, while Supernatural deals with darker and more dangerous supernatural elements. So when they cross over, there's often a theme of the Scooby gang having to adapt to this new level of danger.
Mystery solving also remains a big theme. Even in the face of much scarier and more powerful supernatural forces, the overall goal is still to solve the mystery at hand. The Scooby Doo elements of unmasking villains and finding out what's really going on blend well with the Supernatural aspect of hunting down and defeating evil entities.
One creative storyline could be that the Winchester brothers get stuck in a town haunted by a ghost. The Scooby Doo gang shows up to solve the mystery. Sam and Dean initially think the gang is just a bunch of amateurs, but they soon realize that the gang's skills in unmasking fake ghosts could be useful in their real - life hunting. Another idea is that a demon has possessed one of the Scooby Doo characters, and the Winchesters have to figure out which one and exorcise the demon without scaring the rest of the gang too much. A third could be that there's a cross - dimensional rift that pulls the two groups together to stop an ancient evil that is using both the Supernatural and Scooby Doo universes as its playground.
One idea could be that the Winchester brothers are hunting a ghost in a town where the Mystery Machine gang also happens to be. The Scooby gang initially mistakes the Winchesters for bad guys but then realizes they're all after the same spooky entity. They could team up, with Sam using his research skills and Dean showing the Scooby gang how to handle real weapons (in a non - dangerous way, of course).
There's also 'Supernatural Scooby Doo: The Case of the Cursed Amulet'. In this one, they discover an ancient amulet that brings all sorts of supernatural trouble. The story does a wonderful job of blending the light - heartedness of Scooby Doo with more serious supernatural themes. It's full of action and mystery.
One great Scooby Doo Supernatural crossover fanfiction is 'The Mystery Inc. and the Winchesters' on FanFiction.net. It has an interesting plot where the Mystery Inc. gang teams up with Sam and Dean to solve a mystery involving a haunted mansion and a powerful supernatural entity.
One common theme is mystery - solving. Both shows have elements of mystery, so in fanfiction, it's likely that they'll combine forces to figure out strange happenings. Another theme is friendship. The characters from both shows form new friendships and learn to work together.
One common theme could be how the other characters react to Daphne's pregnancy. Another might be the challenges she faces during the pregnancy while still being part of the mystery - solving gang.
One common theme is mystery. Just like in the original Scooby Doo series, the gang has to solve the mystery of the phantom virus. Another theme is friendship. They rely on each other to get through the challenges posed by the virus.
One common theme is friendship. The male oc often forms strong bonds with the existing Scooby Doo gang members. Another theme is mystery - solving. Just like in the original show, the male oc is usually involved in unravelling spooky mysteries.
One common theme is the rescue mission. The gang comes together to save Daphne from the kidnapper. Another theme could be mystery. Figuring out who the kidnapper is and why they took Daphne.
One great Supernatural and Scooby Doo fanfiction is 'The Mystery Gang Meets the Winchesters'. It combines the spooky elements of both universes really well. The characters interact in a believable way, with Dean and Sam Winchester teaming up with Scooby and the gang to solve a mystery that involves both ghosts from the Supernatural world and the more typical villains from Scooby Doo. It's a fun read that plays on the strengths of both shows.