It could also be due to the lack of proper rest. Merlin is usually depicted as a very busy character in fanfiction. He has duties in the castle, like serving Arthur, and on top of that, he has to use his magic to help those in need secretly. With so much to do, he might not have enough time to rest, leading to exhaustion.
One reason could be that it doesn't have the right format recognition for fanfiction. Fanfiction can have unique formatting styles that are different from regular texts, and Merlin might not be programmed to handle those.
One reason could be his sense of isolation. In many fanfictions, Merlin might feel alone as he has to keep his magic a secret from most people around him. This constant hiding and fear of discovery can lead to depression.
One reason could be to add a new twist to the story. It makes the relationship between Merlin and Mordred more complex and emotional.
One reason could be to protect the person he marries. If she's a commoner, for example, the noble society in Camelot might not accept their relationship. So, they keep it a secret. Another reason could be that the person he marries has some sort of power or identity that could put them in danger if it was known. For instance, if she was a sorceress, in Camelot where magic is feared, they'd have to marry secretly.
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.
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.
One good 'Merlin exhausted' fanfiction could be 'Merlin's Tiring Day' where Merlin has to deal with multiple magical threats in one day and is completely worn out by the end. It shows his struggle and how he overcomes it despite his exhaustion.
One possible reason could be a magical curse. In the world of Merlin, there are many dark sorcerers who might target Arthur. Another reason could be a poisoned weapon. If he was injured during a battle, the poison on the blade could make him sick. Also, it might be a result of some ancient plague that has resurfaced in Camelot.
One possible reason could be the extreme pressure he faces. Merlin has to constantly hide his magic in a world where it's feared and persecuted. This secrecy and the fear of being discovered might have built up to a point where he feels there's no way out. Also, his loyalty to Arthur might play a part. If he feels he has failed Arthur in some way, like not being able to protect him fully from threats, it could lead to such despair.
Well, it could be a culmination of events. Uther's growing distrust of those around him, combined with Merlin's secretive nature about his magic. Merlin might be caught in the middle of a power struggle or a plot against Uther, and Uther, in his quest to protect his throne and Camelot, decides to eliminate Merlin without fully understanding the consequences. This would also create a great deal of drama and conflict for the other characters in the story, which is something fanfiction writers often strive for.