Note: This takes place post-series and post-legend, but should still obviously be considered an AU.
I actually do ship Merlin and Morgana, even if it doesn't seem like it given the content of my previous stories. So, I decided to write something different (Morgana doesn't die in this one, honestly!) which I hope you'll all enjoy.
Arthur was dead.
All that the Great Dragon had predicted to Merlin many years ago, when he was still young and hadn't yet gone through the great pain and grief he was fated to, was fulfilled.
Everything has a beginning and an end, but why did it have to be this way? Oh yes, destiny. How I have come to completely detest that word!
Destiny had guided him to aid Arthur in uniting all Albion and bringing magic back to the land, yes. But it had also cut down Arthur in the prime of his life, made enemies of those who should have been allies, and cost many innocent lives.
Merlin no longer had any purpose, except for waiting for Arthur's supposed eventual return. The final image of his King, dead on a boat heading for Avalon with Morgana, was burned permanently into his memory. He realized truly for the first time, then and there, that he had been used. He, along with everyone else he knew, both good and evil, had been slaves of destiny.
Before the boat passed out of sight, Morgana had given Merlin a look of pure anguish. He knew that, despite how gifted she had become at hiding her true feelings (compared to long ago, when she had an obvious evil face that was quite annoying), that her sadness was genuine. It was as if, in the very same moment, she realized the truth as well and silently lamented over what could have been.
Of all his regrets, Morgana's fall into darkness was the absolute worst.
He remembered Arthur berating him, thinking he had feelings for Morgana, and to back off for his own good due to their two different social classes. Truthfully, while Merlin had gone to her chambers that evening to reassure her that she shouldn't be scared of who she was, he was beginning to show interest in her beyond friendship.
But nothing came of it, since one disaster after another continued to happen to Camelot and he had very little time to be around her. He suspected that Arthur had a hand in keeping him away from her as much as possible for his own protection (Uther would have literally had his head, and Arthur would have had to find a new manservant), but now he'll never know for sure.
And then I killed her...
While he hadn't actually killed her, for Morgause saved her life, it was as if he had. She returned to Camelot a completely different person, consumed by bitterness and hatred for just about everyone and everything except for her sister and Mordred. He tried several times to reach out to her, to try and bring her back... all without success. And now Arthur was dead, and Morgana was gone.
Merlin had plenty of time to think, he had all the time in the world. He thought much of Morgana to the point of obsession, about how everything could have been different if he didn't drive her away.
Needless to say, he cried often. He was alone.
What good was destiny in the end? Arthur died, as I see it, far before his time. And what I did to Morgana was unforgivable! I should have also at least tried to reach out to Mordred while he was still young and steered him off the path he was going! I was such a fool!
And so it was decided, decades later, that destiny be damned.
It would take a very long time to do what he was planning, but there was an abundance of it.
He was going to go back in time.
Merlin knew that it had to be possible. Anything was possible with magic, he just had to figure out how to use it to achieve what he wanted. Any number of things could go wrong and he would be dead in an instant, especially when it came to spells involving the usage of time. Yes, he had time-traveled before but not to the extent he wanted to, and indeed nobody had ever done what he was attempting.
He had to pick a very specific time and place, for he would have only one chance.
Just what was my absolute worst mistake of my life?
Many bad memories flooded into his mind, including Freya's death. It was very tempting for that tragedy to be chosen as his jump point, as she was his first and only real love. They would find a way to be together.
But his thoughts drifted to Morgana. He remembered her laughter and true beauty untainted by the dark, before she had been reborn as his mortal enemy. If the new Morgana had been beautiful, then the old Morgana was simply stunning.
And he had killed her.
It would be too late if he went back to just before meeting Freya, because by then he already had made his worst mistake.
I should have told Morgana about my magic that night and never sent her off to the Druids, Kilgharrah be damned. And Gaius, as much as I loved you like a father, you were wrong.
While it may be thought that his poisoning of her had been his biggest error, in actuality it was just the final nail in the old Morgana's coffin that sent her irredeemably down the road to ruin. No, he should have confessed his biggest secret to her while she was suffering with her new-found use of magic, and helped her as he ought have. He had lied to and betrayed her from the start.
The choice was made.
Several centuries had passed, and Merlin was sure that all the proper spells were developed correctly. At least, he hoped so. If even one variable was incorrect or even slightly out of place, he would likely die in the most painful and horrible way imaginable.
Either way, it would all be over soon. He was tired.
In order for everything to work, he had to think back clearly to the night Morgana visited him in Gaius's study. It wasn't very difficult to do so, for that moment screamed You were wrong! to him for a very long time.
Within a minute, it will all be ready. It is now or never.
Over the passing of hundreds of years, he came to the sad realization that while he cared deeply for Freya, he did not truly love her. If his plan worked, he would still try and save her life if at all possible but would not fall for her again.
There was but one woman he loved, Morgana.
He didn't know if she would ever care for him in the same way, but even if not he would be content to save her from herself. As for her sister Morgause, he would cross that bridge when it was time. Perhaps he could get through to her as well.
Mordred... he had to aid him somehow, not only to prevent Arthur's death at his hands, but also because in many ways he was so much like him. He would be a teacher to both Morgana and Mordred together, for he had much more experience with magic than either of them.
What was interesting about the method of time-travel he was about to use was that, instead of going back in his current body, he would jump into his past self and both would become one. All of his memories and skill would be retained, which would make some of the upcoming inevitable battles much easier.
As for Kilgharrah, Merlin was either never going to release him, or if he did it would be with a magic stipulation that he would not attack Camelot or any of its citizens. He would find a way to kill him if need be, but he hoped it would never come to that.
Merlin knew that the Dragon would be enraged at his sudden changes to destiny, but he didn't care.
Let him be angry! While he did help me at times and even saved my life on more than one occasion, he also made me hurt people I cared about and wanted me to kill a young boy, not to mention all the innocent people he slaughtered when I set him free. No, he will listen to me whether he likes it or not.
Touching a finger to a glowing green stone, Merlin suddenly felt like his body was both on fire and freezing at the same time. The pain was so unbearable that he screamed, and his surroundings began to vanish away.
In an instant, Merlin found himself standing within a room that he had not set foot in for over five hundred years.
He was in Gaius's study. It had worked!
Merlin was disoriented for a few seconds as he gained his bearings, but to anyone looking at him at that time would think that he was about to leap in the air in complete joy.
There was someone there, the Lady Morgana. She was standing directly in front of him, a bit amused at the somewhat odd look on his face.
"Merlin, are you alright?" she asked him.
"Oh, I was just thinking for a moment." A lot longer than a moment, more like years and years, but you don't need to know that right now. Oh, how I have missed you, Morgana!
He knew that this was it, the very moment where everything was going to change. There was never going to be a new Morgana, for he would make sure that the old will never die at his hand. With greater bravery than he had when he was this age the first time, he took one of her hands in his own and looked directly into her eyes.
"Morgana, I also have a secret, and you will never be alone again as long as I live, I promise you this."
As he was speaking those words, he made his eyes shimmer a bright gold and squeezed her hand tighter. From that point on, everything would be different between the two, and the fate of all had been undone and rewritten.
They were slaves no longer.