One possible secret could be that Merlin is a powerful sorcerer from an ancient and powerful magical lineage. Maybe his family has a long - standing connection to Camelot that has been kept hidden.
It could be that Merlin has the ability to communicate with otherworldly beings that are not of this realm. These beings might be guiding him in his actions to protect Camelot, but this connection is something he has to keep hidden from Arthur and the people of Camelot because they might see it as a threat or something unholy.
In some versions of this type of fanfiction, Arthur's reaction is complex. He might be stunned into silence when he first finds out. His mind would be racing with thoughts about all the times Merlin has used his magic to save him or Camelot without his knowledge. After the shock subsides, he may have a heart - to - heart with Merlin. They would talk about the implications of the secret, and Arthur would likely start to view Merlin in a whole new light, as not just his servant but as a powerful ally with a great burden.
Arthur could also feel betrayed. He has trusted Merlin completely, and finding out about his magic might make him think that Merlin has been hiding something huge from him all this time. However, depending on how the fanfiction is written, he might eventually come to understand Merlin's reasons for secrecy.
It could also be due to some past trauma. Perhaps Merlin has been through an experience where Arthur was involved in a way that now makes him flinch. Like, Arthur might have accidentally hurt Merlin during a battle training in the past, and now Merlin flinches whenever Arthur makes a sudden move.
Some fanfictions show Arthur becoming more dependent on Merlin's magic in certain situations. For instance, when facing a powerful enemy that can't be defeated by normal means. This changes the dynamic from just a king - servant relationship to more of a partnership. Merlin, on the other hand, might feel more confident in using his magic openly around Arthur, which also alters their interactions. They could have more equal conversations and decision - making processes.
It could be that Gwen unknowingly has some sort of magical influence over Arthur. For example, if there is some ancient magic tied to her lineage that she's not aware of, and it's causing Arthur to focus only on her and forget about Merlin. Another aspect could be that Arthur's love for Gwen is so overpowering that it's subconsciously pushing out other important relationships, like the one with Merlin.
In this fanfiction, perhaps Merlin discovers that his pregnancy is part of some ancient prophecy. He could then be on a quest to understand the true meaning of it all while dealing with the normal pregnancy woes. He might also face discrimination or disbelief from some in Camelot who can't fathom a man being pregnant, which would add to the drama.
It would likely become very strained. Arthur has been brought up to uphold his father's anti - magic stance. So, when Uther discovers Merlin's magic, Arthur might initially feel betrayed and distance himself from Merlin.
Well, obviously Merlin and Arthur are the main characters. Merlin is the one whose secret as a Dragonlord is revealed, and Arthur is the one who discovers this secret.
One interesting plotline could be Arthur's initial shock and then his gradual acceptance of Merlin's new identity. He might start to see Merlin in a whole new light and realize how much power Merlin truly holds.
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.