Just a quick one shot. I believe that something happened between Merlin and Morgana in series 2 which would make Merlin's betrayal even worse and make Morgana's turning evil (even thought I don't believe that she is evil) have a bit more of a reason. I don't believe that Morgana would go from liking Merlin to hating him so quickly.

This goes along the same lines of S03E02 as it begins and ends the same. The bits in bold are flashbacks.

Who knew

If someone said three years from now
You'd be long gone
I'd stand up and punch them out
Cause they're all wrong ...

...I wish I could touch you again
I wish I could still call you friend
I'd give anything

Who knew by P!nk

Merlin ran round the corner, hoping he wasn't going to see the person who he thought it was.

"You should leave now while you still can." Morgana smirked at him.

Merlin's face dropped. He couldn't help it. Morgause had changed her from the person he knew, the person he loved.

Merlin knew that he still had to try and get through to her "Morgana, please. I beg you. Women and children are dying. The city will fall."

He knew that she loved the people. He should have never had poisoned her. She had changed.

Merlin studied Morgana. She was still as beautiful as she was when she left Camelot.

Oh how he hoped that he could have done something to save her.

"Good" Morgana replied back. She didn't want this. She didn't want the people to be hurt but it was the only way of killing Uther.

Morgana looked at Merlin. Over the time he had changed a lot. The bags under his eyes were darker, his skin paler. He had even filled out a bit more. He poisoned you. He didn't mean anything of what he said.

"No, you don't mean that." If Merlin's face could drop anymore it would have. "I know you. You have a good heart."

"Well people change, or do very unpredictable things to the people they love don't they?"

Merlin looked down at the floor, not being able to hold her gaze any longer.

"I still love you." Merlin's heart was breaking even more.

"Don't lie! You meant none of your feelings."

Merlin had the strength to look at her again. "I meant every word that night."

Morgana was tried. She now knew everything. She had magic and she was a seer.

Not that she was over the moon because she was right under Uther's nose.

But she knew who she was and the magic that ran through her veins, it wasn't something to be frightened of.

A knock on the door drew her from her thoughts.

She strode across the room and opened the door.

"Merlin"

"My Lady."

Morgana lets Merlin in and closes the door behind him.

"I wanted to check you were ok." Merlin said once he was inside. He turned to look at her.

Morgana smiled. He was such a good and loyal friend. "I'm fine. What was said at the woods..."

"You can trust me, Morgana. I won't tell anyone." Merlin smiled at her.

"Thank you, Merlin. I know now who I really am. And it isn't something to be scared of. Maybe one day people will come to see magic as a force for good."

Merlin smiled even bigger at her. "Yes, maybe they will. Morgana, I ..."

Morgana looked at Merlin, hoping he would carry on.

"Morgana, I don't know how to say this."

Merlin face gave him away. He was having a conflict inside.

"Come on Merlin, you can tell me."

"Morgana, I think I love you. I am glad that you are alright and always want to be by your side."

Morgana looked at him. "And I think I love you too. But nothing can happen. Uther would have your head."

Merlin looked down at the floor. He knew that but he had to tell her of his feeling or he would have told her about his magic.

Merlin broke the silence "Erm...It's good to have you back."

Morgana just smiled at him, know that she had hurt him.

"Thank you, Merlin."

She opened the door and him out.

"Sleep well." She said to Merlin only to have him smile back at her. She had to do something about their feelings.

Morgana thought over that night.

"Didn't you mean your feelings? You were the one that pushed them. We were happy."

"Until you betrayed me."

"I didn't want to."

Merlin poured the hemlock into the water skin. He didn't want to do this and it was breaking his heart.

"Here, have some water." He held out the water skin, hoping she would take it so it was dragged out any longer.

"I'm not thirsty."

Merlin's heart sank even further. It was slowly killing him inside.

"If we get out of here, you may not get another chance to drink." He would give her any excuse.

"If we get out of here."

Merlin handed her the water skin, but she puts it down by her side.

Merlin went and listened to Arthur fights in the corridor. He didn't have much longer.

Merlin had an idea, he walked past and picked up the water skin and pretends to drink it.

"Here." Merlin's heart couldn't take it anymore.

"I'm fine."

"No, you have some before I finish it."

Morgana sighed. He was very persistent. "Thank you." She said smiling at him.

Morgana brought the water skin up to her lips and drinks.

Merlin turned around and his heart broke. He could live with himself.

He heard that Morgana started to have trouble breathing.

Morgana looked at the water skin and then at Merlin.

Merlin wipes his eyes and then turns to face her. His heart was definitely broken and so was hers.

Merlin knelt down and tried to hold Morgana, it was going to be the last him he could, as she struggles to breath.

Both hearts broken by betrayal.

Merlin was grateful for Morgause saving Morgana so he could see her again but he didn't want her like this.

"You watched me as I was dying in your arms."

Merlin was close to tears.

"Your words and feelings meant nothing." Morgana's words were laced with poison. She didn't like hurting him but she could never forgive him for what he had done.

"And what about yours?"

Morgana looked confused.

"You and Alvarr."

Merlin watched as Morderd ran into Morgana's open arms, and Morgana giving the crystal to Alvarr.

He watched and listened to their conversation.

"It's my hope that with time Mordred will master the Crystal. And when he does, we will strike Uther down. Uther and all who serve him." Alvarr seemed pleased by her work.

"All who serve him?" Morgana seemed worried at that.

"If we are to win this war, there can be no half-measures. I see this troubles you." Alvarr looked at her with concern. Merlin didn't like this one bit.

"Yes. Yes, it does." Merlin knew that Morgana cared for many people in Camelot.

"My Lady, we fight for our very survival, as do you. The boy. He told me you have magic. You need not be afraid."

Morgana looked shocked at this. "I know. I'm sorry. I've become so used to concealing the truth."

"Believe me, I understand what that feels like."

"Every day I must look Uther in the eye knowing that if he were to discover who I really am, he'd have me killed."

"You have been very brave."

Merlin wanted to laugh. He hadn't been alongside her as she had gone through everything.

"I don't want to be brave. I just want to be myself. I don't want to be alone anymore."

What did she mean I don't want to be alone? She wasn't alone, she had me.

"You are not alone. You're here with us. You need never be alone again."

Merlin watched as Morgana and Alvarr leaned in.

He quickly left after that, not seeing Morgana pull back.

"Nothing happened between me and Alvarr. How did you know about it?"

Merlin froze, he couldn't allow her to know about him following her.

"You have been following me longer than just the other day." It was a statement and not a question.

Morgana mask started to slip. She had hardened herself to him but now that she knew that he thought she had been unfaithful to him, that he had followed her.

Merlin couldn't lie to her any more. "I was worried about you but now only do I realise that I was starting to lose you when Morgause had shown up."

Morgana knew after then she had become more rebellious but before then she had been rebellious.

Morgana grabbed the manservant into the alcove.

Merlin smiled at Morgana. "We have to be more careful. Arthur almost found us out last night."

Morgana smile back and moved closer to Merlin. "I don't care. I wanted you and I want you now."

Merlin closed that gap between them and kissed her.

They had many meetings like this. Her dragging him into an alcove, him waiting for Gwen to leave then sneaking into her room. Even when Arthur wasn't in his room.

Merlin smiled into the kiss. He was happy.

This beautiful woman wanted to be with him. Yet it couldn't happen.

They broke apart.

"My room tonight."

Morgana walked out of the alcove, swinging her hips.

Merlin just stood and stared at her, watching her go.

Tonight was going to be good.

At dinner, Merlin had to stand behind Arthur, which was opposite Morgana.

Morgana's favourite game was to try and make Merlin feel uncomfortable.

She would give him looks which he couldn't help but squirm under her gaze. If he poured her wine then she would whisper seductively into his ear.

Uther wouldn't notice but on the rare occasions Arthur noticed so Morgana had to turn it down a notch.

Merlin was too much of a gentleman. He had been brought up like it. He would never go any further with her but she enjoyed the nights snuggled up next to him. Somehow he made the dreams go away and the visions.

Morgana held onto Merlin tighter that night. She was scared that she was going to lose him. She didn't want to lose him, not after he brought her so much happiness.

"So the nights in my chambers didn't mean anything to you?" Morgana asked. She knew that they did just she wanted to hear him say it.

"Of course Morgana. You aren't alone and I know that you don't want to harm anybody."

"Oh am I not? I have magic, Merlin. Uther hates me and everyone like me. Why should I feel any differently about him?"

"When did I say anything about Uther?"

"You said that I wasn't alone but I am."

"You aren't. Anyway you of all people could change Uther's mind, but doing this? Using magic like this will only harden his heart."

"You don't have magic, Merlin. How could you hope to understand?"

Only if you knew. Only if I had told you. Merlin couldn't take this anymore soon he would tell her of his magic "I do understand, believe me. If I had your gifts, I would harness them for good. That's what magic should be for. That's why you were born with these powers."

Morgana couldn't take this anymore. She was fighting between killing him and kissing him. "You don't know what it's like to be an outsider. To be ashamed of how you were born, to have to hide who you are. Do you think I deserve to be executed because of who I am?" She prepared herself for the answer. She hopes he would say no.

"No. It doesn't have to be like this. We can find another way."

Morgana let go of the breath she didn't know she was holding. What other way was there? There was only one way and Uther had to die, that's what Morgause had said. "There is no other way."

Merlin nodded, understanding. He stepped back as if in defeat.

He dashed around the pillar to try and get the Rowan staff from the other side.

Morgana used her sword to knock his out of his hand.

Morgana started to advance on him. She couldn't allow Uther to win. Merlin started to back up.

"What are you going to do? Kill me?" Merlin hated to say it and hoped that it wasn't true.

"You don't think I can?" Morgana said in her seductive tone. Morgana, you're going to kill the man but talking to him like you're going to kiss him.

"If you're going to do it, make it quick." Merlin knew it was a way of getting revenge of what he did to her and it would also help his aching heart.

Morgana slashes at Merlin. Merlin ducks and picks his sword up from the floor.

Merlin continues to block Morgana's attacks.

Morgana manages to disarm Merlin again.

Merlin still manages to avoid her attacks.

Morgana flung her sword at Merlin and fell off balance.

Merlin manages to his behind a tomb. It was now or never.

"Feoll bu brand!" Merlin whispered, hoping she didn't hear or see his eyes flash gold.

The spell cause part of the crypt roof to fall, landing on top of Morgana.

Merlin stood up and walked over to her. Morgana was knocked out but still breathing.

Merlin picks up the closest sword and runs towards the staff.

"Snæde!"

The sword sliced through the staff. The magic quickly leaving the crypt.

Merlin walked back over to Morgana. He knew that she would never forget this.

He would never stop loving her.

Merlin kneeled beside her. He knew that this would be the last time he could do this.

He gentle pressed his lips on hers.

"Goodbye Morgana."

He quickly got up and left the crypt, leaving behind the Morgana that he used to love as well.

Everyone wondered why Merlin kept getting even paler and the bags under his eyes getting darker.

It was love. Who knew that it wasn't meant to last.