Note: This takes most of Series 3 into account, only Morgana takes the initiative here in order to steal the throne, with terrifying results for all. Semi-Dark!Merlin here, be warned.
Arthur was supposed to be the Once and Future King to unite the land of Albion, but how could he be if he was dead?
Morgana had succeeded in killing both him and his father by one of the most simplest of means: poison. Nearly every night the three had dined together, and it was as easy as tainting their drinks with the help of slight-of-hand and misdirection, so nobody would notice her quickly pouring three drops of a green liquid into each goblet. It was slow-acting, taking hours to have full effect, and was nearly untraceable. For those that would check on them the following morning, it would appear as if they had died suddenly in their sleep.
Merlin had done so, screamed, and vomited all over the floor of the Prince's room before collapsing in a sobbing, miserable heap. He had failed his ultimate destiny, and he knew exactly who was responsible. By now, she had likely already taken the crown from Uther's dead head and was in the process of inviting her sister into the castle walls, ready to proclaim herself as the new Queen.
He didn't care about anything anymore. There was no point in keeping his magic a secret, for Morgana and Morgause would soon to try and kill him anyway once they came across him, and he wanted to make them pay. He was going to kill them both very slowly and as painful as possible, in front of all Camelot as witnesses, after making them admit what they had done to the King and Prince.
He wasn't safe in Arthur's room because the witches were sure to soon look there, and he needed to get away before he was caught.
Merlin was a mess, and could hardly breathe as he stealthily creeped out of the room and down many hallways, many of them underused, to avoid being seen. By some great fortune, he managed to make it to Gaius's study undetected. It was already ransacked, with Gaius himself nowhere to be seen, and Merlin's Sidhe staff and spell-book were both stolen from their hiding places. He had been extremely lucky that he had left to attend Arthur at the precise time that he did, or he most likely wouldn't still be alive. Sadly, it was very probable that Gwen and Gaius, the other two people in Camelot he truly cared for, were already both dead and nothing could be done for them, just like Arthur.
It was only a matter of time before they found him, and he thought that he should just let them.
Morgana was the only legal heir to the throne that was still alive, at least the only one that he had known of. If she died, Camelot would be thrown into anarchy and war would probably erupt to determine a new ruler, and many more lives would be lost. In addition, enemies of Camelot would see it as the prime time to attack to try and stake a claim of their own, in particular Cenred, who did not deal with his previous loss against the kingdom well.
He thought of something else that he did not earlier, when his grief was still too raw and fresh: Kilgharrah! He could help him escape!
Merlin cried telepathically with all his magical power to the Dragon, hoping that he would answer him and come to his aid. Despite being a Dragonlord, Merlin and Arthur's destiny was very important to the Dragon, and he feared that he would be left there to die for his failure.
It wasn't long before that part of the castle was reduced to ruins as Kilgharrah swooped down and tore through the roofs and walls in order to reach Merlin, quickly scooping him up and flying away from Camelot as fast as he was able. Merlin thought he heard several shouts and gasps, at least one from Morgana herself, before he passed out in the Dragon's claws.
When he had awoken, it was night and he could tell that he was on a mountaintop far from where he had been previously. It was a sure sign that all that he had experienced earlier was no nightmare, and he broke down crying once more.
"Merlin, Merlin! Stop it at once! Shedding tears will not bring Prince Arthur back to life!"
The Great Dragon was towering over him as he looked up from where he sat. He figured that he was either going to be burnt alive or eaten, and if he tried to escape there was nowhere to go but far, far down to his death. Still, he listened to the Dragon and stopped, deciding that he at least wanted to die with some of his dignity left intact.
"I failed him. I failed him, and he's dead, along with probably everyone else I care about. You must be very angry with me."
"Yes, I am very angry with you, that is no lie. The future that I have seen that the two of you would have created is gone, and will never be. But not all hope is lost, Merlin. Albion can still be united and peace can reign, but only if you do exactly what I say. If you do not, or if you stray just a little, then there will be no hope for anyone. I've warned you time and time again about the witch, and you did not listen! You should have left her to die and not forced me to help save her life!"
"I know, Kilgharrah. You're right and you always have been, and I'm truly sorry for not listening to you, and using you for my own ends. I thought that Morgana could still be saved somehow, that there was even a sliver of good still inside of her soul, but I was wrong and look where that led to! I want to kill her and her sister like nothing I ever have before! I never wanted any of this to happen! Why? Why did all this happen to me?"
"You are a man, and I am a dragon. Men and dragons often do not think alike, young warlock. The witch, Morgana, was once a gentle and beautiful woman who would lay down her life for those she loved. And I know what you are thinking, that it is your fault that she ended up the way she did, and you are partially correct. However, her hatred for Uther Pendragon would have in time completely corrupted her no matter what you would have done or not done, which is why I encouraged you to not get close to her. I did not want to see you hurt, Merlin, and I express deep sorrow at your current state."
Merlin had indeed loved Morgana, but she was dead and cremated as far as he was concerned. What remained of her was little better than an empty shell.
"Is there nothing that can bring Arthur back? Do you not have some great, powerful dragon magic that can achieve such a thing?" asked Merlin.
"I'm afraid not. Nothing can truly bring back the dead, magic included. There is nothing that you can do for him anymore, and he has passed into Avalon along with his father. I have seen another future in which you are instrumental in salvaging a part of the original destiny of Camelot and all Albion, but in order to do so you will have to pay a terrible price."
"Except... except for my mother, I have nothing left. I will gladly pay any price to try and do what is right."
"Are you absolutely sure of that, Merlin?" asked the Dragon, who smirked as he spoke. "You may not think so once you have heard what I have to say. There is but one option open to you, which will also allow you your revenge upon the witches."
Merlin wanted to kill Kilgharrah.
The Great Dragon's plan was indeed one that would require a great sacrifice in order to succeed, but until he heard exactly what had to be given he had not realized the magnitude of it.
And now, he was rotting in a cell in Camelot, waiting for Morgana to come to him.
Both Merlin and the Dragon determined that Morgana and Morgause's arrogance would be their downfall, that instead of killing Merlin on sight they would capture him and blame him for the murders of the King and the Prince before being publicly executed, in order to take suspicion away from Morgana and to strengthen her reign.
They were right, and after Merlin had 'surrendered' and was briefly tortured by Morgause's magic, he was dragged in chains by guards loyal to Morgana into the dungeon. On the way, he noticed that none of the knights that were friends of and loyal to Arthur and Uther were around, figuring that they had all been put to death swiftly already.
He had to be extremely careful that nobody touched any part of his skin with their own, or the plan would fail and he would not get another chance.
Before long, Morgana entered, dismissing the guards. She wore Uther's crown and carried Arthur's sword in her hand, fully intending on taunting him at his failure and torturing him to near-death, but she would never get the chance to do so.
Merlin rushed towards the bars, and shoved his hand through them to touch Morgana's neck. She recoiled and tried to back away, but it was already too late, for he had made contact with her. Both screamed in unbearable pain as a white smoke emerged from Merlin's mouth, quickly entering Morgana's and settling deep within her, after which the screaming ceased. Merlin then fell to the floor, dead.
It took a few moments for him to get his bearings, no... her bearings, and realize that it had worked.
The Dragon's plan was to use a variant of the dark magic that Cornelius Sigan used to possess his victims, and told him that it could only be used on someone who was alive, meaning that Arthur was not a candidate. He had to be absolutely sure that he didn't touch anyone besides Morgana, or he would be forever trapped within that person's body, instead of being forever trapped in Morgana's body as was intended.
He had done it, he had given up his own life and identity in order to save and bring peace to the free world, but outside of the Dragon (and his mother, who he fully planned on telling), nobody would ever know.
Merlin was dead. Morgana was who she would be for the rest of her life.
Morgana's soul was gone, she had no idea what had happened to it or where it went, and thought that it was probably best that she didn't know. At any rate, Merlin's soul had taken complete control of Morgana's body. She was also pleased to discover that she still had her own magic and not Morgana's, because it was a part of one's very essence.
Using Arthur's sword, she decapitated Merlin's head from off his body in order to cover what had really happened, and left with the sword still bloody. She was about to pay a visit to her dear sister, which was going to be quite a short one.
Morgause argued with her that she should not have killed Merlin yet, but Morgana countered her. "He taunted me, calling me worthless and saying that he'd wished that the poison had acted faster and that I'd died before you could save me. Did you know that he was also the one who knocked me down that flight of stairs? He laughed at that. He had gone completely insane, and I couldn't take any more of what he was saying, so I silenced him forever."
Having been distracted by the conversation, before Morgause could so much as reply she found Arthur's sword plunged through her heart.
"And now I'm silencing you forever. Maybe you will shortly meet your sister, I honestly don't know. Goodbye."
Morgause was dead before she hit the stone floor, and her blood quickly began to pool.
"Citizens of Camelot, many lives were lost in the needless slaughter and sorcery of Morgause over one year ago. She had bewitched me and I could do nothing but watch as she murdered the King and his son in cold blood, my mind and body were not my own to control. To be honest to all of you, I never wanted to be Queen of Camelot, and I despised my father for not acknowledging me as his daughter. But for all his crimes and hypocrisy against magic, he did not deserve what happened to him, for he was a lonely and broken old man deeply set in his ways. The ban against magic will never be reinstated as long as I am Queen, for I am a sorceress myself and had to hide that fact from all for a long time, and suffered greatly for it."
"There is one among the lost who I must mention. His name was Merlin, and he sacrificed his life to save each and every one of you, and for Camelot to prosper. May his name be remembered always."
The assembled people below cheered, and the Queen gave a light bow before leaving the balcony and retiring to her chambers. As soon as she entered, she removed the crown from her head and threw it across the room, where it made hard contact with a wall and rebounded off it, undamaged.
Morgana collapsed upon her large, comfortable bed, the same which once belonged to the King of Camelot, and wept into her pillows. Her entire life was a lie. She was not Morgana, she only looked like the now-dead witch, and despite her crowning as Queen and the expected further peace and prosperity to come, it would not bring Arthur or any of her friends back to life.
Gaius had survived long enough to hear the truth from her, before saying that he was proud that she had made such a sacrifice for the greater good and for everything else she had done to protect everyone over the past few years, before his older body gave out and died. He was entombed with high honors, along with Arthur, Gwen, Uther and many other fallen Knights that had tried to fight back against Morgause and Morgana, to no avail.
Merlin's body, at Hunith's request, was brought to her homeland of Ealdor and quietly buried there. She now lived within the castle, serving as the Queen's personal maidservant. Hunith loved that which was now her daughter unconditionally, and always would. Many noticed how close the two women were to each other, but the truth of Morgana would never be known by anyone else. Everyone knew that Hunith had been Merlin's mother, and thought that her appointment to the Queen was a high honor in remembrance of the brave man who had fallen by the sword and hatred of Morgause.
Morgana didn't know where she would go from that point onward. She was now Queen of Camelot and had been so for a year, something that should have never been but now was, and would love and serve her people as best as she was able until her death. She would be a far better and more just ruler than Uther Pendragon had ever been, but at the same time would not tolerate any true threats to her kingdom. Mordred would soon die by her hands, for the Dragon had said that he would bring chaos to Albion and eventually kill her, if not stopped.
Having learned her lesson at not heeding his advice before, she decided to make the first strike and eliminate him before he could grow into a man and become too powerful for her to handle. Her destiny and reign was but a mere shadow of what could have been, if Arthur had lived to be pronounced King, but it was still better than nothing. Morgana would not fail everyone again as she did before.
She was Queen Morgana of Camelot to all, except to her mother when in private and to the Great Dragon, both of which still referred to Morgana as Merlin when in conversation with her. For the rest of her life, she would have the face, body and voice of the murderer who had so cruelly taken everything away from her, and be reminded of it every single time she looked into a mirror, glanced downwards at her chest or spoke. As far as she was concerned, her identity of Merlin was as dead as her original body was. She could no longer use his name around all but two, and naming herself 'Morgana' began to come with such ease and without thought that she started to think of herself by that name even when around them, and encouraged them both to do so as well. Merlin's voice in her mind and thoughts was rapidly being replaced by Morgana's softer, lighter tone, and she knew that one day it would be gone forever.
She suspected that Kilgharrah's intentions had been every bit as malicious despite being also the salvation of Camelot, and that her state was a great punishment for letting Arthur die before his time. He was supposed to have been the rightful ruler of Camelot and a King of legend, but now she was forced to be a Queen, in a body and life she had never wanted or even dreamed about in her worst nightmares.
Drying her eyes with her fingertips, Morgana rose from her bed and retrieved her discarded crown from the floor. She had indeed salvaged destiny and paid a terrible price for doing so, just as the Dragon had predicted.