One interesting storyline could be Merlin using his magic to help the Trollhunters in a battle against an ancient and powerful troll enemy. Maybe he could use his knowledge of spells to create a magical barrier that protects the trolls and humans working together. Another could be a time - travel plot where a Trollhunter is sent back in time and meets Merlin, and they have to work together to change something in the past to save the future of both the troll and human worlds.
A great storyline might involve Merlin teaching the Trollhunters some of his unique magic. For example, he could teach them how to use magic to communicate with nature, which could be useful in finding hidden troll lairs or predicting the movements of enemy forces. Also, a story where Merlin's past mistakes in dealing with magical creatures come back to haunt him in the Trollhunters' world, and he has to make amends with the help of the Trollhunters would be really engaging.
How about a crossover with the Percy Jackson series? The Trollhunter could meet Percy and his friends at Camp Half - Blood. Since both deal with mythical creatures, they could exchange knowledge about different mythologies and fight side by side against monsters that are drawn to the power of trolls and the demigods.
One idea could be that the characters from Trollhunters and 3Below have to team up to fight a common enemy that is threatening both their worlds. Maybe an ancient evil that has the power to destroy Arcadia and Akaridion - 5. Another could be a story where the technology of 3Below is combined with the magic of Trollhunters to solve a mystery that has been plaguing both species for centuries. For example, a mystery about a long - lost artifact that has the power to reshape their universes.
Maybe the technology from '3 Below' gets mixed up with the magic in the Trollhunter universe. For example, Aja and Krel's advanced tech could malfunction in the Troll world and create some unexpected chaos. The Trollhunters would then have to help them fix it while also dealing with their own troll - related problems.
Another idea is a crossover with 'Avatar: The Last Airbender'. The Trollhunters could meet Aang and his friends. They could combine their powers to defeat a common enemy that has the ability to disrupt both the balance of the four elements and the Troll world's magic. For example, they could fight a dark spirit that is draining the magic from the Troll world and using it to spread chaos in the Avatar world.
The magic in Merlin's world is often more traditional, based on spells and incantations. In the Trollhunters' world, the magic seems more innate to the trolls. If they were to interact, Merlin's spells could potentially enhance or disrupt the natural magic of the trolls. For example, a spell of his might accidentally block a troll's ability to use its natural camouflage magic.
A cool plot could be that an interdimensional rift opens up and sucks in some of the characters from both shows. They find themselves in a strange in - between world where the rules of both their universes are mixed. The Trollhunters' magic doesn't work quite the same, and the technology from 3 Below is malfunctioning. They have to figure out how to get back to their respective worlds while also fending off strange creatures that are native to this new world.
One idea could be that Merlin uses his magic to help Sherlock solve a case that seems to have supernatural elements. For example, a series of murders where the victims all seem to have died from some unexplainable force. Merlin's ability to sense magic and his knowledge of the old ways could give Sherlock new perspectives on the case.
One idea could be that Merlin uses his magic to help the Avengers in a battle against a powerful magical enemy. Maybe he disguises himself as a normal human at first and then reveals his true powers when the situation is dire.
One interesting 'trollhunters fanfiction' story could be about an alternate universe where the trollhunters are from different time periods and have to team up. Another might focus on a character who was never fully developed in the original and gives them a more in - depth backstory. There are also those that explore romantic relationships between the characters in a new and unique way.
A third storyline could involve Merlin facing the challenges of being in a position of power as a sorcerer in Uther's court while still being a servant at heart. He has to deal with the snobbery of the nobles who look down on him as a sorcerer, yet he has to use his influence to protect Arthur and Camelot. He might also have to make some tough decisions, like whether to expose a fellow sorcerer who has committed a crime, or to try and rehabilitate them in secret.