I normally don't like genderbent stories, but something about a female Merlin really appeals to me. Also, the idea of Merlin (or Merlyn) being stuck in an unwanted love triangle is very amusing. If you are a Merthur or a Merdred shipper, then this is not the story for you.
Edited on 6/25/2018
It All Comes Down to a Girl
So Merlyn was very confused. The entire trip back home was spent pondering this new mystery. Well, that and ignoring Mordred. And trying not to go insane. But, back to her confusion. So here's the deal: Merlyn enters cave. Said cave has nearly dead Druid in it. Said Druid shows her a vision of a mysterious dark haired fellow killing Arthur (she rather thought that she'd look something like that if she were born a boy). And then said mysterious dark haired fellow suddenly turns up, revealing himself to be Mordred, the boy who everyone and her mother seemed to be warning her about (and by mother, she means the dragon Kilgharrah). But that's not the confusing part. The confusing part was that Mordred decided to backstab Morgana (literally) and save Arthur (and her too, after he got the king to safety he raced back to get her only to find her with a glowing alien thing). So, the question of the hour was this: if Mordred is destined to kill Arthur, why did he save him? Question two of the hour was: and why won't he shut up?
"Emrys? Emrys? Emrys, are you mad at me? Please talk to me, Emrys. Emrys, did I do something wrong? I saved Arthur, Emrys, I thought that was what you wanted. Are you upset I left you alone while I got Arthur to safety? I'm really sorry about that, I wanted to get you first, but I didn't want to be suspicious. Emrys?"
Hence the ignoring part. Nobody else knew what was going on, of course, because Mordred was speaking telepathically. Gwaine seemed to have noticed the twitch Merlyn got in her left eye after the second hour, however, and was now trying to figure out what was bugging her.
After the third hour, Merlyn finally snapped. In a dangerously calm voice, she thought, "Mordred?"
"Yes, Emrys?" And dear god, he sounded like an excited puppy.
"Shut. Up." Merlyn gave everyone a thorough glare the rest of the day, and Mordred went from being an excited puppy to a kicked one.
When they finally got back to Camelot, Arthur made Mordred a knight. Merlyn simply narrowed her eyes at him and glared suspiciously. He was destined to kill Arthur one day, and she didn't trust him in any way, shape, or form.
Unfortunately, that didn't impede him in one bit. Everywhere she went, he always seemed to be there, trying to talk to her, trying to figure out why she didn't trust him. She had to find a spell to block him from her mind because he wouldn't stop speaking to her telepathically at all hours of the day. It wasn't until Merlyn had vented her frustrations to Gwen that she finally realized what was going on.
"Oh my, you really are oblivious, aren't you?" Gwen asked with a laugh. "The same thing happened with Arthur!"
"What are you talking about?" Merlyn asked.
"Well, it's obvious that Mordred likes you," Gwen replied. "He probably has some sort of attachment from when you saved him all those years ago."
Merlyn's eye twitched. "So how do I get him to leave me alone?"
Gwen shrugged. "How did you get Arthur to leave you alone?"
"I hit him on the head and called him a prat. And even that hasn't worked so well."
The serving girl chuckled. "Well, maybe you can just try explaining to him that you're not interested."
Merlyn nodded. "That might work."
It did not work. If anything, it only made Mordred more insistent. And, unfortunately, Gwen wasn't the only one who noticed.
"Mordred seems very fond of you," Arthur said one day while Merlyn was cleaning his chambers.
Not liking where this was going, Merlyn answered, "He likes you, as well. I think he has a sort of attachment to us from when we saved him all those years ago." She didn't bother with mentioning that Gwen said that first.
"That's not what I meant," Arthur pressed. "He likes you."
Merlyn shrugged. "He's a young boy just barely out of his teen years. Who knows how long he was with those bandits. I was probably the first girl he's seen in awhile, so it was either me or Morgana, and, well…" The 'Morgana's insane' bit was left unsaid.
"It's inappropriate," Arthur growled.
"How so?" Merlyn asked, slightly amused.
"You're five years his senior!"
"Four, actually," Merlyn corrected him. "And you're four years my senior. But you don't seem to have a problem with that."
"It's not the same," Arthur grunted, looking very put out.
"Yeah, it kinda is," Merlyn retorted. She finished up and left after that, not keen on dealing with a jealous Arthur at the moment. He really needed to get over her. Maybe marry Gwen. Poor girl's been horribly lonely since Lancelot died. She and Arthur would be good for each other.
Of course, Merlyn couldn't keep this up forever. She was walking down the corridor when a hand suddenly shot out and grabbed her arm, pulling her into an empty chamber. And there was Mordred. He did not look pleased.
Merlyn heaved a dramatic sigh. "I thought we've been over this. I just don't like you that way, and you really need to-"
"That's not it," Mordred cut in, glaring at her. "I want to know why you don't trust me. Everyone else does, and they all know that I was once a Druid. Hell, even Arthur does, though he's been giving me a lot of these death glares lately…"
Merlyn sighed again, this time a bit regretful rather than annoyed. She wanted to like Mordred (not in that way, just in the general, friendly way one feels towards a person who is trying very hard to make her, at the very least, not hate him). He was, despite her doubts, a rather sweet boy. He had eventually gotten the hint and toned back on the stalking (okay, he wasn't really stalking, but it was about one or two steps below that), and he didn't get her flowers anymore. He was friendly with the other knights, and so far a decent warrior even without magic. All in all, not a bad fellow.
Except for the whole 'destined to kill Arthur' thing. But see, that was the whole problem here.
"Alright," she heaved. "You really wanna know why I don't trust you?"
"Yes!" he answered loudly, crossing his arms and looking at her expectantly.
"You sure? 'Cause you're not gonna like it."
"I don't care," he replied. "Whatever it takes to earn your trust, I'll do it."
Merlyn sighed, yet again (she'd been doing a lot of that lately). "Okay. I don't trust you because a dragon told me it was your destiny to kill Arthur. I also don't trust you because a Druid actually showed me a vision of you killing Arthur. And I don't trust you because you have a strange sort of bond with Morgana. But mostly the first two reasons, which is sort of one reason. But it's a very good reason," she insisted, not really noticing the growing horror on Mordred's face.
"It's my destiny to kill Arthur?" he cried, taking a step back and clutching a hand to his chest. "But...but…"
"Oh…" Merlyn frowned at him. "You didn't know."
"How could I have possibly known that?" Mordred demanded, glaring at her.
"Well, I kind of assumed that it was your nefarious plan to get close to Arthur and then kill him, so, yeah…"
"Well, I'm not going to kill him!" Mordred declared boldly.
"Yes, and once upon a time I thought that Morgana could never turn into a psycho murderer sorceress yet here we are," Merlyn answered with a shrug.
"So you're just writing me off, even though I haven't done anything yet?" Mordred demanded. "Can't we stop this?"
Merlyn held her hands up in apology. "Look, buddy, I've tried changing destiny before, I really have. I always just ended up making sure it happened. So I don't try to change the future anymore. I just do whatever I can to make sure the bad futures don't happen."
Mordred shook his head. "That's not any different."
"It's different," Merlyn insisted. And then she noticed the dejected, horror-ridden look on the poor boy's face and attempted to comfort. "Um...there, there... I'm sure you won't kill Arthur...I hope," she added in a mutter to herself. "Just so long as he doesn't do anything to make you bitter and angry or you don't do anything to make him bitter and angry and...oh…"
"What?" Mordred asked, trying to move closer for a hug, but Merlyn wasn't having it.
"Oh," she repeated. It all made sense now. "I'm caught in the love triangle of death. Literally." She shook her head and turned back to Mordred. "Look, I know you're probably jealous of Arthur, but that's no reason to kill him."
Mordred's brow furrowed. "Why would I be jealous of Arthur?"
Merlyn, being the idiot she was, replied, "Well, 'cause, he's in love with me. And you-"
"What?!" Merlyn realized a moment too late that she shouldn't of said anything at all. "He what?!" Mordred's eyes were blazing, and suddenly he understood everything. All those angry looks Arthur was sending him...those times when he'd sling an arm around Merlyn's shoulders and then give him a look. "Well, if that's how it's gonna be," he stated in a deadly serious voice. Abruptly, he turned and marched out of the room, fully intending to face Arthur right then and there.
"Wait!" Merlyn called after him and following him out into the corridor. "Killing him won't fix anything, I don't like either of you! At least not like that!" Mordred wasn't listening as he rounded the corner, eyes set on Arthur's chambers. After realizing he went the wrong way, he promptly whirled around and marched in the other direction. Merlyn let out a groan and grumbled, "See, this is why I don't try to change destiny!"
I've seen a few stories out there with a love triangle between Merlin, Mordred, and Arthur so this is my take on it. Chapter two features: Uther returning from the dead and is disappointed by what he finds.