Rin Tohsaka could also be a good crossover character. As a mage in the Fate universe, she could be intrigued by Arthur's arrival. She might try to study his magic or enlist his help in the Grail War. Their relationship could start off as a bit of a power struggle as Arthur is not used to taking orders from a young mage like Rin.
Saber from Fate/Stay Night would be an obvious choice. Since she is also related to the Arthurian legend, there could be a lot of interesting interactions between them. They could compare their experiences as king, or even fight side by side against a common enemy.
The theme of redemption also pops up. If Arthur is placed in a darker or more morally ambiguous world, his quest for justice and honor can be seen as a form of redemption for the new world he's in, or it can be a test of his own values as he faces new challenges.
Maybe Arthur Pendragon gets transported to the Fate world and his presence disrupts the normal balance of power. The mages in the Fate universe might see him as a threat or an opportunity. He could end up being a wild card in the Grail War, not bound by the normal rules of Servant summoning. His noble phantasm, Excalibur, could be a game - changer in battles against other powerful Servants.
There's also 'Arthur and the Star Wars Galaxy'. This one is a wild ride where Arthur Pendragon somehow ends up in the Star Wars universe. He teams up with Jedi and Sith, and his code of chivalry creates some unique interactions within the Force - using world.
One possible reason could be a misunderstanding. Maybe Merlin did something that Arthur misinterpreted as betrayal or dishonesty. For example, if Merlin was secretly helping an enemy for a greater good that Arthur wasn't aware of at the time.
Well, in such a fanfiction, they could team up against a common enemy. Maybe an ancient dark force that has been awakened in both their times. Their combined knowledge of magic from different eras would be a great asset.
A fanfiction that stands out is 'Arthur and Merlin: A Different Path'. This one takes a different turn from the original storyline. It imagines a world where Arthur discovers Merlin's magic much earlier. This changes the whole dynamic between them, and they face different challenges together. There is also 'The Adventures of Merlin and Arthur in the Enchanted Forest'. It's full of exciting quests and the development of their friendship.
The main characters could include the heir's family members from the Pendragon side, even if they are long - dead, they might appear in memories or visions. Dumbledore could also be a main character as he is a very important figure in the Harry Potter world. He might guide the heir, knowing about their special heritage and seeing how it could be beneficial in the fight against evil. Another possible main character could be a villain who wants to use the heir's power for their own dark purposes.
A good 'Arthur Pendragon Merlin fanfic' often has a strong portrayal of their friendship. For example, it might show how they support each other through difficult times. Like when Arthur is facing a tough battle, Merlin is there with his magic to help, and vice versa.
One common theme is gender role reversal. Since Arthur is typically male in the original legends, fanfictions with a female Arthur often explore how she navigates a world that has certain expectations for men. For example, she might face different challenges when it comes to leading knights or being accepted as a ruler.
One possibility in Hermione and Arthur Pendragon fanfiction could be a story where Hermione uses her modern magical knowledge to help Arthur Pendragon in his time. For example, she could introduce new spells or ways of using magic that were not known in his era. This could lead to a series of adventures as they face challenges together, like defending Camelot from a new dark magic threat.