Well, it could also imply that there is a work titled 'Merlin' and some aspect of it, such as a new official canon, a new interpretation of the story, or a new development in the related media, has made it difficult for fanfiction writers to continue with their previous ideas. For example, if a new Merlin series completely changes the backstory or relationships of the characters, it can break the fanfiction that was based on the old understanding.
Merlin could be heartbroken. He might retreat into himself and become more withdrawn. After all, he has a deep bond with Arthur, and this sudden break - up would be a huge shock.
Jealousy could be another factor. Arthur might be jealous of Merlin's magic or the attention Merlin gets from others because of it. This could create tension and ultimately result in a break - up in the fanfiction.
In a more humorous take on the 'Merlin tied to a bed' fanfiction, it could be that Merlin has fallen ill and the overly - protective Gaius has tied him to the bed to make sure he rests. Merlin, being the active person he is, complains constantly. Arthur comes to visit and teases Merlin about finally being still for once. Meanwhile, Merlin tries to convince Arthur to let him loose, promising that he'll be fine. Eventually, Gaius relents and unties Merlin, who then immediately starts bustling around the room.
If Merlin died in the fanfiction, it could trigger a series of tragic events. The balance of power could tip, and the villains might seize the opportunity to attack. It could also bring out hidden strengths in the remaining characters as they try to cope with the loss.
One more idea is that Merlin is tied to the bed in a dream - like state created by an ancient magic. In this dream world, he is faced with his deepest fears and insecurities. His friends in the real world notice his strange behavior and try to wake him up. Merlin, while in the dream, has to find the source of the magic that is binding him and break free. Through his inner strength and the memories of his friends, he manages to do so and wakes up, having learned more about himself and his magic.
If Merlin is a Dark Lord in fanfiction, it could be an interesting exploration of the 'nature vs. nurture' concept. Maybe he turned dark because of the constant fear of being discovered and persecuted for his magic. His actions as a Dark Lord might include taking over Camelot or exacting revenge on those who wronged him in the past. It gives a whole new perspective on his character.
Another possibility is that it could be a new character created specifically for the fanfiction. A character who wears a mask for some secretive purpose, and when the mask breaks, it sets off a chain of events that are unique to the fan - created storyline.
One possible reason could be a magical curse. In many Merlin fanfictions, magic is often used as a plot device. A dark sorcerer might cast a spell on Merlin to make him forget certain things, perhaps to prevent him from using his powerful magic to oppose them. Another reason could be a self - imposed forgetting due to trauma. Merlin has witnessed and endured a great deal of pain and suffering. To protect his own mental state, his mind might subconsciously block out certain memories.