Maybe it's a mysterious figure from Merlin's past. Perhaps he had an encounter with a powerful magical being, and some kind of spell or pact led to the pregnancy. It could be a long - forgotten event that now resurfaces with this unexpected pregnancy.
Another possibility is that it's a result of Merlin's own magic gone awry. His powerful magic could have created a life force within him without the need for a traditional father figure. This would add an interesting twist to the story as he has to deal with the consequences of his own magic's actions.
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.
Well, it could be Arthur in a more creative and alternative fanfiction. Their deep bond could be taken to a whole new level with this unexpected turn of events.
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.
Socially, it could be difficult for him. If others find out that he still has feelings for Lily and she's pregnant, he could face ridicule or be the subject of gossip. Also, depending on his relationship with Lily's partner, there could be conflict. He may have to face the fact that he has to keep his distance more than ever to avoid causing trouble for Lily and her unborn child.
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.
I recall a fanfiction named 'Merlin's Immortal Fate'. In it, Merlin discovers he's immortal when he survives a fatal wound that should have killed him. This discovery changes his perspective on life and his role in Camelot. He starts to use his immortality to protect the kingdom in ways he hadn't thought of before. There's also a fanfic where his immortality is tied to a magical spell cast long ago, but I can't remember the exact name right now.
It could be that the pregnancy is a sign of a prophecy coming true in a very unexpected way. In the wizarding world, prophecies often have strange and convoluted ways of manifesting. Harry might discover that this pregnancy is linked to a greater destiny for him and the wizarding world. Maybe the child he's carrying will be a powerful force for good or evil, depending on how things play out. His relationship with Ginny would also be greatly affected. She would have to deal with her own feelings about Harry's situation, and they would need to work together to face this extraordinary event.
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.
In fanfiction, if Uther finds out Merlin has magic, it could lead to Merlin's immediate arrest. Uther is known for his extreme hatred of magic in the Merlin series. He might see Merlin as a great threat and try to execute him, just as he has done with other magic - users.
Often, Gwaine reacts with acceptance. He's not the type to shun Merlin just because of his magic. Instead, he'll likely embrace it as part of who Merlin is. He could say something like 'Merlin, your magic doesn't change a thing between us. You're still my friend.'