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.
I really like 'Avalon's Arthur in Fate Fanfic'. In this story, Arthur has a deeper connection with Avalon, his mythical resting place. It gives a fresh perspective on his powers and his relationships with other Fate characters. Then there's 'Arthur's Allies in Fate'. This fanfic focuses on Arthur forming new alliances and how those relationships shape his journey in the Fate world. 'The Pendragon Legacy in Fate' is also good. It explores how Arthur's legacy affects the present - day Fate universe and the characters within it.
One popular character paired with Arthur in Fate fanfic is Saber. Since she is an incarnation of Arthur in some versions of the Fate series, they often have complex interactions. Another is Merlin. He is Arthur's mentor and advisor in the original legend, so in fanfics, they are often shown having deep conversations and Merlin guiding Arthur through different situations. Also, Artoria is commonly paired with Arthur as they are both related to the Arthurian legend and can have interesting dynamics in the Fate fanfic world.
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.
One great Arthur Pendragon hurt fanfiction is 'The Wounded King' which delves into his emotional turmoil after a major battle. It shows his struggle to regain his strength both physically and mentally.
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.
One great 'Arthur Pendragon Merlin fanfic' is 'The Once and Future King' -esque story where Merlin's magic is a key factor in Arthur uniting the kingdoms. It shows their deep bond and how Merlin uses his powers to protect Arthur in a very creative way.
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.
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.