One possible consequence is that Morgana could use this knowledge to blackmail him. She might force him to do things for her using the threat of revealing his magic to others in Camelot. Also, if the wrong people find out that Morgana knows about Merlin's magic, it could put Merlin in a very dangerous position. His friends like Arthur might turn against him, thinking he has been lying all this time.
He might face distrust from Morgana at first. She could think he has been using his magic against her without her knowledge.
She could be shocked at first. After all, Merlin has been hiding his magic for so long. Maybe she feels a sense of betrayal initially, but then she might see an opportunity to have an ally in the world of magic.
He could face Morgana's distrust if she takes his secrecy the wrong way. Maybe she'll think he has other motives for hiding his magic from her.
Arthur could also feel betrayed. He has trusted Merlin completely, and finding out about his magic might make him think that Merlin has been hiding something huge from him all this time. However, depending on how the fanfiction is written, he might eventually come to understand Merlin's reasons for secrecy.
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.
For Merlin, there are both good and bad consequences. On the bad side, some of the more traditional and anti - magic people in Camelot might try to oppose him. However, since Arthur now knows, he has a powerful ally. Arthur can protect Merlin from those who would do him harm. Also, Merlin can now be more open about using his magic for the good of Camelot, which is a positive change.
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.'
In some fanfictions, Naruto could find out in a very emotional way. For example, his daughter might be in danger, and when he discovers she is his, his feelings of love and the need to protect her are intensified. He might also struggle with the fact that he has missed out on part of her life so far. He'd then start to make up for lost time by spending as much time with her as possible, teaching her ninjutsu and sharing his own life experiences.
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.
After James discovers Severus' abuse, Severus may experience a range of emotions. He might be initially reluctant to accept James' help, given their history of animosity. But if he does accept, it could lead to a transformation in his self - esteem. He could start to believe that he is worthy of protection and care. In terms of his relationships at school, it could either improve his standing if the other students follow James' lead in protecting him, or it could make things more complicated if there are those who oppose James' new - found support for Severus. His academic performance might also be affected. If he feels more secure, he could focus better on his studies, but if he is dealing with the fallout of the abuse being known, it could be a distraction.
She might be shocked at first. Given that in the original story Morgana has her own complex relationship with magic, seeing Merlin's magic could stir a mix of emotions in her, like envy or a sense of relief that she's not alone in her magical abilities.