My fellow wiki users, I believe that Morgana loved Merlin for most of the series, I have no shame admitting I am a Mergana shipper, but I have evidence, and to be honest I believe the writes squandered a great romance possibility
Series 1 I believe that Morgana loved and probably still loved Merlin for most of the entire series, and this started around episode 8. Previously she probably just fancied him as a friend from afar, jealous that Gwen had someone so willing to fight for her as Merlin did in 01x03. “She is a lucky woman.” and telling Arthur that she couldn't imagine any person loving her so much. She was grateful that someone cared as much about her only friend as much as she did. It’s obvious she knew the power she possessed with her looks and her status, so she probably had a hard time trusting people with sincere intentions in caring her and her feelings.
She was surprised by Merlin and him helping her with Mordred after 01x08. Especially because he was Arthur’s servant. This was of course the beginning of their relationship, and when she subconsciously realized that Merlin is one of the only people she could truly trust.
His act of helping her meant so much to her that she actually was the first people to jump to the opportunity of helping Merlin protect his mother and village. I think it said a lot for the writer to choose GWEN asking MORGANA why Arthur was helping the village, and for Morgana to say that it’s because it’s for the same reason: Merlin. A lot of other things could have been said with the same message, but they decided to have MORGANA state it was because of MERLIN.
Series 2 I think she realized she loved Merlin in episode 03 - my favorite Mergana episode and one where you can truly see their amazing chemistry.
The fact that she tells Merlin about her nightmares after knowing him for less than a year. Obviously she would never tell Uther, despite her being his Ward, and even though she has a complex relationship with Arthur and shows that she goes to him because she knows she can trust him to do some things, she never goes to Arthur about this particular issue. Which I think says A LOT. Merlin’s acts of kindness truly baffled Morgana - the servant who worked closely with two people who despised magic. She not only trusted him with her nightmares, but she trusted him to tell the truth about the druids. He could have easily led her into a trap, but she trusted him enough to know that he wouldn’t do that.
When Merlin found her in the camp she was probably shocked in a good way that he went out of his way to find her, and for her to ADMIT her powers, the ONLY person she did to in this point of time, without second guessing. And as Arthur’s servant, some part of her still probably doubted that he will turn against her, but when he smiles, and says he understands….you can just see it in her face. Since the death of her father she has never trusted or felt so much sincere love. That a servant has shown her more compassion than her “family” has. That this servant is risking his life so he can tell her that the king is looking for her. I will argue that she was about to kiss him in this moment. The look she gave Merlin is exactly the same as she gives Alvarr in episode 11.
As they were rushing to escape you see Merlin risk his own life for her. Again, he is sacrificing himself for her secret and she is in awe. She proclaims that she “will never forget his.”
When she returned in the castle they share a very sweet and innocent moment together. She allows him, in her room, at night, in her pajamas. We have to remember the timeframe here…that is pretty big. Again, she doubts him (this is how insecure she is as Uther’s ward) and the smile she gives when he says that her secret is safe. The awkwardness of this scene…that they both realize that it’s night and they are in her chambers…alone.
When he say’s “uhm” and she looks up at him…that my friends is the head tilt of a “you should kiss me…make the first move.” When he says it’s good to have her back instead, she still is touched by his kind words, but it’s also in the moment that she realizes that he is a servant and she is a ward. That nothing can ever become of them at this moment in time. She also looked extremely disappointed that he did not lean in to kiss her. And to be honest, while there is no evidence of my next statement, I wouldn’t doubt that part of her hatred for Uther stems into the fact that as his Ward that she can’t be with the person she loves.
Of course, little moments throughout season 2 when Morgana is afraid of people finding out about her magic, and she instantly looks over to Merlin, as if saying “protect me” is very blatant. She also looked at Merlin in disbelief when Aredian accused him of sorcery, and the camera panned away to show she was concerned for him from the expression on her face.
In episode 11 Morgana wanted nothing more than to be herself with people…Merlin being her only anchor in Camelot. Alvarr was just using her, a prime example of what she is use to, but I like to point out the scene when she is telling Alvarr of how she is so alone, and when he tells her the same thing that Merlin has. He goes in to kiss her. And she does too, but then she stops… why? Is it not ironic that he almost told her the exact same thing as Merlin, in the exact same place. She probably realizes this and that’s why she stops. Notice how her next words is that she should return to the castle… who do you think she was thinking of?! Merlin
The heart-breaking episode 12. The pivotal moment. A lot can be debated on if Morgana knew what was going to happen to her friends, I like to believe that if anything she thought Morgause would only kill Uther, but obviously she didn’t know she was the source. She probably knew Morgause had something to do with it, but that’s it. I don’t think she would have gone through all that trouble of saving Uther if she really knew what was going on. Anyways, so at the beginning of this episode she probably still has her thoughts on Alvarr and just wanting to escape her life. And then Merlin appears and ugh, I hate and love this episode.
Despite Arthurs relationship with Morgana (Which is pretty good) he suspects Morgana, Merlin (despite all he knows of her) does not. At first you see Morgana once again looking at Merlin with that plea in her eyes “protect me”, and that’s exactly what he does. Look at her just stare at him in utter disbelief as he lies to Arthur…his beloved Arthur.
When Merlin leaves and she is protecting Uther (who she could have easily killed, mistaking that this was part of the plan) just sits down… shocked once again by Merlin…and her feelings.
After moving Uther and being close to Merlin again, Merlin runs off to get servant clothes, leaving Morgana alone again with her feelings, slowly realizing what must be taking place. When Merlin returns. The look on her face…the I was “worried about YOU” - not the prince of Uther.. but YOU just seals her love for him. Her comment of him being a “good friend” only makes the next couple of scenes worse.
She probably would have bartered with Morgause to spare Merlin, and probably Arthur, if she had the chance.
But Merlin poisoned Morgana and the hurt and betrayal in her eyes. The fact that her insecurities that she thought she had washed away, flooding back as she stares into the soul of the only man she truly loved, and who she felt truly loved her.
Series 3 After she returns to the castle, fully knowing what Merlin did, I think that is truly what caused her to go evil. Knowing the fact that once again, someone else chose other people compared to her. Especially the person that she loved… it was the last straw.
If you had doubts on her feelings she had, and still has for Merlin, then this scene only erases your suspicions. When Merlin rushes underground and confronts Morgana, time is literally stopped… when she asks Merlin if she should be killed for who she is and he replies “no”… her stare…
Her eyes were basically saying “I loved you, for this very reason, why did you betray me?”
She is about to cry in this scene. It pains her that he not only says that “we can find another way.” but that she has convinced herself that “there is no other way”. Lets also note that she just stands there. She knows what he has come to do but she doesn’t want to move.
She loved Merlin because when she was with him she didn't feel alone.