Perhaps there's a plotline where Merlin discovers that his bond with Arthur is not just a matter of loyalty and friendship, but is actually a magical bond that was created by an ancient magic long before they were born. And as they face various challenges, this bond either strengthens or is put at risk depending on their actions.
Obviously, Merlin is one of the main characters. He is a powerful wizard with a great destiny.
Another plotline might involve Merlin coming back to find Camelot in chaos. His return then becomes a journey of restoring order, not just through his magic but also by reuniting the people and rebuilding their trust in the kingdom. He might have to deal with those who have misused power in his absence.
One interesting Fate Merlin fanfiction could be about Merlin guiding a young and inexperienced mage in the modern Fate universe. This could involve him using his ancient magic knowledge to help the new mage face challenges.
One interesting plotline could be Merlin's early days in Camelot, his struggles to hide his magic while trying to prove his worth to Arthur. Another might be his encounters with different magical creatures that are not shown in the original series and how he manages to deal with them.
One interesting plotline could be Merlin using his magic in modern times to secretly protect Arthur, who is a powerful businessman or politician. For example, he might use magic to prevent assassination attempts on Arthur.
Perhaps Merlin has to save the knights from a curse. He could go on a long journey to find the ingredients for an antidote while facing many obstacles along the way. He might have to outwit evil spirits or solve difficult riddles to get what he needs to break the curse on the knights.
One common plotline is when Merlin reveals his true identity to Arthur in a moment of great danger. For example, when Camelot is under a powerful dark magic attack and Merlin has no choice but to use his magic openly to save everyone.
One interesting plotline could be a new prophecy related to blood magic that only the main characters can decipher. It might involve a hidden blood bond between some of the Hogwarts students that gives them unique powers.
One interesting plotline could be the knights and Arthur facing a new, powerful dark magic threat that only Merlin's unique powers can help them overcome. They might journey to a far - off land in search of a magical artifact Merlin has foreseen as the key to victory.
One interesting plotline could be the discovery of Harry's connection to Merlin and how it affects his magic in ways not explored in the original series. For example, he might have access to ancient spells or a deeper understanding of magic's origin.