A forgotten ancient entity that was sealed away long ago in both worlds. It has now broken free due to some recent events in both HTTYD and Spyro's universes. This entity is made of pure dark energy and can possess both dragons and other creatures. It wants to plunge both worlds into eternal darkness and rule over the chaos it creates.
A powerful dragon - mage hybrid could be the main antagonist. This creature could have the ability to control both the dark magic from Spyro's world and the power of the more menacing dragons in HTTYD. It wants to rule both worlds and is using its magic to create chaos and turn the dragons against each other.
An evil viking sorcerer who has learned about Spyro's world and wants to harness the power of the gems there. He teams up with some of the more hostile dragons in HTTYD like the Red Death (if it somehow survived) and plans to use their combined strength to take over both Berk and Spyro's realm. He uses dark magic to corrupt the minds of the dragons and the vikings.
It could be an evil dragon that preys on Spyro's troubled state. This dragon might try to manipulate Spyro into doing bad things or lead him further astray from finding peace with his troubled soul.
Kaos could be a great main antagonist. He might see Dark Spyro's power as a tool to finally achieve his evil goals and try to manipulate him.
Maybe the main antagonist is a sorcerer from a far - off land in Spyro's world. This sorcerer is jealous of the attention the human is getting and the potential power they might bring. So, they start causing chaos and trying to turn the other creatures in Spyro's world against the human and Spyro. They could use illusions and dark spells to make things difficult for our heroes.
It could be an ancient evil force that wants to use the Dark Master Son's power for its own dark purposes. This force might see Spyro as an obstacle in its plan to dominate the world.
The main antagonist might be a dark sorcerer. This sorcerer has put a spell on Spyro's mother long ago, trapping her. He doesn't want Spyro to find her because he fears that together they will be strong enough to break his power. He uses his minions to try and stop Spyro during his journey to find his mother.
Perhaps the vikings of Berk accidentally open a portal to Spyro's realm while exploring a new area. Spyro is intrigued by the vikings and their relationship with dragons. Meanwhile, Hiccup tries to understand Spyro's abilities and how they can be used to improve Berk's defenses. They could team up to rescue some baby dragons that were captured by an evil force from both their worlds.
It could be an old enemy of Spyro who has been plotting his downfall for a long time. This antagonist might be another dragon who is jealous of Spyro's popularity and power at the academy. He could manipulate the situation to make Spyro turn evil and then use him as a weapon against the Skylanders.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
Obviously, Harry Potter himself would be one of the main characters. He could be the one to first encounter Spyro and start the whole adventure. Spyro would also be a main character, with his unique abilities and personality. Hermione could also play a big role as she would be very interested in learning about Spyro's world and how his magic works. And Ron, with his loyalty and sometimes comical nature, could provide some light - hearted moments during the more serious parts of the story.
A powerful demon from another dimension could be the main antagonist. This demon could be attracted to the power that Sinbad wields in the Magi world and wants to steal it for himself. He could start causing chaos in both the world Sinbad is from and the world he's been transported to in the crossover.