Well, it could be that the Naruto gang gets transported to the Scooby Doo world. Maybe they team up to solve a mystery that involves some sort of ninja - like villain in the Scooby Doo town. Naruto could use his shadow clone jutsu to help search for clues while Scooby and Shaggy are off running from the 'ghost' that's really the bad guy in disguise.
A great plot could be that there's a food - themed mystery. A new, strange food is making people act weird in town. Scooby Doo and Shaggy are, of course, very interested in the food aspect. Tom and Jerry are also drawn to it because it smells so good. Tom wants to keep Jerry away from it, but they all get caught up in finding out where the food is coming from and why it has such an odd effect. The gang uses their detective skills, while Tom and Jerry's constant chasing around the food sources actually uncovers some hidden secrets about the mystery food.
Well, perhaps the Scooby Doo gang could time - travel to the era when Jurassic Park was being built. They start to notice strange things happening, like the dinosaurs seem to be more intelligent than they should be. It turns out that a disgruntled employee is using some kind of new technology to control the dinosaurs and make them cause trouble. The gang has to work together, with Scooby and Shaggy providing some comical relief as they are chased by T - rexes and Velma and Fred solving the mystery.
Well, perhaps the plot involves a female Shaggy who has a special connection to one of the villains. Maybe she knew the villain from her past and this knowledge helps the gang understand the motives behind the spooky happenings. She could also use her charm and wits to get closer to the truth than the others in the group. As the story progresses, her relationship with the other characters, like Fred, Velma, and Daphne, might evolve in interesting ways as they all work together to solve the mystery.
In this fanfiction, it could start with Scooby Doo and Shaggy being chased by a 'monster' which turns out to be a large, misunderstood Pokemon. The Pokemon trainers then come in to help calm the Pokemon. As they get to know each other, they find out that there is a mystery surrounding a series of disappearances in the area. The combined skills of the Pokemon's powers and the Scooby gang's sleuthing lead them to a hidden lair where a mad scientist is trying to use Pokemon DNA to create an army of super - monsters. They must work together to stop this evil plan.
Well, in a fanfiction, the Hex Girls might be trying to unlock an ancient musical power. They believe it's hidden in an old, abandoned theater. Scooby Doo and his friends join them on this quest. However, the theater is full of traps and ghosts. As they explore, they learn that the ghosts are actually the guardians of the power. The Hex Girls must prove their worthiness through their music, and with Scooby Doo's help in distracting the ghosts, they are able to unlock the power and become even more amazing musicians.
One possible plot could be that Naruto and his friends end up in the world of Scooby Doo. They team up with the Mystery Inc. gang to solve a mystery that involves some sort of ninja - related magic. Naruto could use his shadow clone jutsu to help search for clues and his combat skills to protect the gang from the villain.
Well, perhaps there could be a crossover where Scooby and Shaggy accidentally eat some magic cupcakes in Equestria that give them the ability to talk to the ponies in a special way. Then they discover that there is a mystery surrounding a disappearing magical element in Equestria. The rest of the Mystery Inc. gang shows up to help, and they all join forces with the ponies like Rainbow Dash and Fluttershy to find out what's going on and save the day.
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).
One idea could be that Naruto and the gang from Scooby Doo team up to solve a mystery in a ninja - haunted village. Naruto uses his ninja skills like shadow clones to search the area while Scooby and the gang use their detective skills to look for clues.
Perhaps in a fanfiction, the gang could be exploring an old haunted mansion. Velma discovers some strange clues that seem to be related to a long - lost love story. As she and Daphne research more deeply, they start to feel a strange attraction towards each other. Eventually, as they solve the mystery of the mansion, they share a kiss, which is a celebration of their new relationship as well as the solving of the mystery. It could also add a layer of complexity as they wonder how the rest of the gang, especially Fred and Shaggy, will react.