One idea could be to have characters from different Skylanders groups team up to face a new, super - powerful villain. For example, the Trap Masters and the Giants could combine their forces.
Another plot idea is a crossover within the Skylanders universe where characters swap their elements. So a Fire Skylander has to use Water - based powers and adapt to a new playstyle, which would create a lot of comical and challenging situations in the fanfiction.
A more complex plot could involve Skylanders from different generations getting trapped in a time - loop that is slowly draining their powers. They must figure out how to break the loop and who is behind it, all while dealing with their own personal rivalries and friendships that get tested in this strange situation.
Perhaps the Skylanders enter the Naruto universe. They could be mistaken for some kind of new ninja jutsu or summoned creatures at first. Then, they work together with the ninja to protect Konoha from a major threat, like an invasion of powerful demons. The Skylanders' different abilities, such as Spyro's fire - breathing or Stealth Elf's stealth, would add new elements to the battles in the Naruto world.
One idea could be a story where a young Skylander discovers a hidden dragon egg. The Skylander then has to protect the egg from the evil forces in Skylands who want to use the dragon for their own dark purposes. As the egg hatches, a bond forms between the Skylander and the dragon, and they go on adventures together to stop the villains.
One idea could be Dark Spyro's struggle to control his dark powers while trying to protect his friends. Maybe he has to face an ancient evil that only his dark powers can defeat, but using them risks corrupting him completely.
One idea could be that Spyro and Cynder have to team up to face a new, powerful enemy that threatens the Skylands. They start off a bit at odds due to their different personalities but gradually learn to work together better.
A really interesting plot could be that Spyro and Cynder accidentally swap powers. This would lead to a lot of comical and also challenging situations as they try to figure out how to use each other's abilities and also deal with the villains who take advantage of their confusion. They would have to rely on their friendship and understanding of each other more than ever.
One idea could be Dark Spyro struggling to control his dark powers while trying to fit in at the academy. He might accidentally cause chaos during training sessions.
A plot could revolve around Spyro and Cynder having to train a group of new Skylanders recruits at the academy. They have to use their unique skills and teamwork to get the recruits up to par. This could involve teaching combat skills, as well as lessons about loyalty and friendship within the Skylanders community.
Another plot could involve Cynder getting lost in a mysterious part of Skylands. Spyro then has to search for her while facing various challenges. As he looks for her, he discovers that Cynder has a special connection to an ancient prophecy. The two of them then must work together to fulfill the prophecy and save Skylands from a great danger.
One idea could be Spyro discovers a new power within himself that allows him to communicate with ancient Skylanders spirits. He then has to use this power to stop an evil force from awakening an ancient, powerful and dangerous monster. Another could be Spyro gets transported to a parallel dimension where the Skylanders are all different and he has to find a way back while also helping this new world with their problems.
A great fanfiction could revolve around the origin of the Swap Force. You could explore how the concept of swapping parts came to be in the Skylanders world. Maybe it was a result of an ancient magic experiment gone wrong or right, and how this ability has shaped the battles and relationships in Skylands.