Note: This is an AU taking place after the first few episodes of Series 3, and thus there are some spoilers for that.
There was a bit more I felt like I must add to this story, so here it is. I don't know if I will continue to write any more about this dark version of Merlin (I think it's probably best if it ends here), but thanks for the reviews.
The reaction to Morgana's treachery was immediate. The King, having been struck with what looked to all as a very powerful blast of magic, slumped back against his throne and slid down to the floor.
That was bad enough, but what happened next would be etched into the minds of all in the throne room forever.
An over-zealous guard, completely loyal to Uther, rushed forward with sword drawn in hand. With one careful swing, her head was soon removed from her shoulders, dropping directly in front of Uther. Luckily for the King, he was not conscious at the time to see such a sight.
Morgana's headless body turned around to face the guard. A still stunned Merlin realized that his careful scheme had suddenly changed, and very rapidly canceled all the spells animating her. Her body, having nothing supporting it anymore, fell.
The throne room was complete chaos for hours afterward. Nobody knew why the Lady Morgana had suddenly gone berserk and attempted to murder the King with magic, but for most seeing someone they had so dearly loved and trusted be decapitated before their eyes was even worse.
Gwen was one who took it badly, having been present near Morgana. She broke down and would not stop crying, until Arthur stepped in to console her, and both left. Under other circumstances this may have been frowned upon, but nobody cared that day.
Merlin didn't know what to think. What took place was completely unexpected, even for him. He had an elaborate speech scripted for Morgana to say after her attack, and various taunts and hateful things to say to Uther, Arthur, and himself. Everything had been planned right up to her burning to death on her pyre, but any number of things could have gone wrong. His spells weren't perfect, nor were his emulations of Morgana's mannerisms.
I suppose things have gone better and much easier than I'd hoped, but to see Gwen like this...
After he canceled the great number of spells on Morgana, as well as those affecting Uther and Gwen, Merlin felt light-headed for quite a while as his energy began to return to him.
He went to his room under the guise that he was overwhelmed at all that happened, which was in part true, but it was mostly so he could be alone. Alone so he could reflect on what he did, and what he would do from there.
As much as he despised Uther for his hatred and genocide of those who have magic, Merlin could not help but to feel utter pity for him after he regained consciousness and was told about Morgana.
What little was left of Uther Pendragon after the death of his wife was completely and utterly broken. He had loved and had taken care of Morgana as his own daughter, and while they often did not agree eye to eye on certain things, he had never expected something like this to happen.
Her remains were ordered to be taken outside of the city. Everyone knew what that meant. Outside of Camelot was a place where the bodies of sorcerers, regardless of their method of execution, were burned to the bone and later crushed into ash. Said ash was then thrown into a deep crevice nearby, where it would remain forever.
All of this, according to Uther, was to prevent them from being brought back to life or used for other nefarious purposes by other practitioners of sorcery. He was mostly incorrect in his assumptions (for he knew little about magic), but nobody dared to question him.
And so, the story of the Lady Morgana ended as so many others did, a pile of ash down a deep, dark hole.
The King also decreed that nobody talk about her ever again, on pain of death. He also decided to send even more knights to further hunt and exterminate the Druids, because he blamed them for everything. He blamed all of those who practiced magic, and he would not stop until they were all discovered and killed. Only his hatred for magic was left now.
Days later, Merlin remembered something that he had not thought of since the day he confronted Morgana. Someone.
He knew that Morgana and Morgause were still in direct contact, but he didn't dare try and spy on them for a fear of a repeat of what they tried to do to him before, or worse. By now, Morgause had to have known that something was wrong, and most likely had heard of Morgana's death.
He had stolen a sword from the armory and hid it in his room, during the time he was having nightmares about Morgana. He thought that she might decide to attack him while he slept, so he had it as a last resort.
Merlin had hoped that the nightmares would stop after Morgana was gone, but they didn't. They worsened. Most of them involved an incredibly pale and dead-looking Morgana saying Why? to him over and over again. A few variations had her say this from her severed head at Uther's feet as everyone in the throne room glared at him accusingly. He knew that these dreams would never stop, but would haunt him for the rest of his life.
I had to do it. I hated it, but I had to. She could have killed Arthur otherwise, and I'd have failed my destiny. And in the end, destiny is all I have.
Taking the sword, he left his room, past a sleeping Gaius and further onward in the castle, until he was well outside of Camelot. Sneaking around undetected was another thing that kept getting easier for Merlin, aided by the fact that the castle guards seemed to be blind.
It wasn't long before he came across her in a clearing, and he drew his sword. He wasn't going to let her speak for long, because he had gone there for only one reason.
Morgause, meanwhile, was plotting how she would avenge her sister and watch in glee as all of Camelot burned in flames. She also knew that this coward in front of her was responsible for her death, as he had nearly done it before. He would be begging for death before the end.
"You did it, didn't you? Morgana is dead by the guiding of your hand!"
"Yes." he replied. "And you are about to die the same way she did."
Having completely underestimated Merlin as any possible threat to her, the last sight Morgause saw was a magically-propelled sword flying towards her neck, and then nothing.
He engulfed her body and decapitated head with a magical flame, which unlike the fire used at that place, would destroy everything, including her bones and the armor she wore. After a few minutes, any and all trace of Morgause was gone. After retrieving his sword and cleaning her blood off, he sheathed it and returned to Camelot, planning on going to sleep.
He couldn't. A part of his mind rebuked him for the dark path he had taken, that he would be consumed by it and lost. But the rest of him knew that for Arthur's sake, and for all Albion, he had to do what he had to for the greater good.
What he did to Morgause was yet another secret to be added onto his ever-growing pile. Merlin was afraid that he wouldn't be able to keep track of what to say and what not to say to different people, some of which knew none of his secrets and others different levels thereof. He knew that Morgana's demise was something he couldn't ever tell anyone, because he would never be forgiven for it.
It wasn't bad enough that he had killed her, but he had violated her. Morgana's body was his to control, and she would have done anything he wanted. She was nothing more than a puppet that bent to his every whim, and he had been no better than horrible men that force themselves upon women. While he would never, ever do that to anyone, rape was the closest analogy to the horrible magic he had used on her corpse.
How could he move on after all of this?
Merlin remembered when he first came to Camelot, in what seemed to be a whole other lifetime ago. While his life was not the greatest, and work was hard (Arthur seemed to have a fondness at making Merlin muck his stables), he was happy and except for having to hide his magic, relatively carefree. He wished for those days to return, but he knew it would never be so.
All he could do is wear a mask and pretend that all was well. To Arthur, Gwen, Gaius and everyone else who regularly noticed him, Merlin seemed to be perfectly fine and cheerful as he always was. It was yet something else that became even easier to Merlin, lying.
Merlin was just as dead on the inside as Morgana had been.