Perhaps some of the snooty nobles who look down on Merlin and constantly try to get him into trouble. They could be making fun of his clumsy ways one too many times and he just snaps and hits them with a shoe. It would be a moment of satisfaction for the readers who don't like those arrogant characters.
One possible plot could be that Merlin gets really frustrated with some bullies in Camelot. They've been taunting him about his magic or his lowly position. In a moment of rage, he uses magic to make a shoe fly and hit them as a warning. This could lead to a series of events where he has to hide his use of magic more carefully while also standing up for himself.
Arthur could visit Merlin in the tower. He might be curious about what Merlin does in his secret place or he could be in need of Merlin's help and follows him there.
The ruling class or the nobles associated with the castle would be in big trouble. Their power base would be gone. They might try to hunt Merlin down or they could be forced to seek shelter and help from other lords. This would cause a shift in the power dynamics in the region.
It could be Morgana. She has been known to be an antagonist and has a vendetta against Camelot and those associated with it. Poisoning Merlin would be a way to weaken Arthur's most powerful ally.
Arthur could be the cause. He often bosses Merlin around and doesn't fully understand Merlin's capabilities. His constant demands and lack of respect for Merlin's intelligence might push Merlin to the edge. For instance, when Arthur makes Merlin do dangerous and pointless tasks without any regard for his safety.
Well, fanfiction often offers new and exciting scenarios. For Harry, who has been through so many dangerous and challenging situations in his own story, fanfiction can provide different takes on his life and abilities. It could show him in situations he never faced in the original story. The same goes for Merlin. He has his own set of adventures, and fanfiction can expand on those or put him in new and unexpected situations.
It could be for comedic effect to lighten the mood and add some fun to the story.
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.
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.
Merlin was a powerful wizard. He was Arthur's mentor and advisor.