This is an Alternate Timeline that starts during "To Kill the King", and goes into a different direction from there on; it works under the assumption that Morgana didn't immediately find allies against Uther.
Gwen/Morgana, background Gwen/Arthur and Gwen/Lancelot.

Disclaimer: I don't own BBC's Merlin etc.

Clad in Shadows

The king will no longer listen to her.

Her rage burns into nothingness, turns on itself and feeds on her isolation. Morgana knows how to whisper if she can't shout: she has in her repertoire soft words as sharp and painful as daggers, sweet punctured comments full of venom; but she has never learnt to bear in silence.

She finds Gwen still in her room, sitting by a window and seaming at a dress of hers with application. Her eyes, when she glances up at her approaching mistress, are red but dry, and her weak smile genuine.

"It's alright," Morgana says quickly, when her handmaiden puts the dress aside and moves to stand up. "Don't –"

Gwen pays her no heed; gently, she takes the scarf from her shoulders, removes the heavy necklaces and bracelets and sets them aside; Morgana stands still and lets her, until finally she can't help putting both arms around her.

"Gwen," she says softly. "I'm sorry, I should have –"

"No," Gwen just says, and she falls silent.

Gwen holds her, caresses over her back, again and again, soothingly, tries to ease the painful tension in her shoulders, as she has so often before: every time Morgana came, furious and powerless, from a confrontation with Uther; every time she's watched – she always watches – an execution she deems unfair. She feels her own sadness and tension weaken as she calms Morgana, fingers playing through her hair and over her face delicately, until Morgana gently takes hold of one of her hands to kiss her fingertips, and then her chin, and then her mouth.

"Stay here?" she asks, in between kisses. Gwen nods.

Much later, she falls asleep on Morgana's bed, exhausted, arms still wrapped around her; for the first time, unable to make the tension in Morgana's body disappear.

When she's sure she won't wake the other woman, Morgana gently frees herself of her embrace and briskly stands up. If she wants to keep her safe, she has to act, and as soon as she can.

xxx

The king calls for her. He doesn't apologize, not Uther, but he's seeking her forgiveness, she can tell; he's thanking her for her resolute resistance; he's admitting to wrongdoing.

Morgana doesn't say she forgives him, but vows to try and mend things between them; her voice is soft and cold and measured, and he sees no deception in it.

Her hate, she feels, vanishes at this, as she witnesses his regret. But her resolve doesn't; she knows now: as long as Uther lives, he will be a danger to all the ones she loves.

(One day, the same will be true for Arthur.)

xxx

Morgana is a shadow in the streets of Camelot.

Enveloped in a long coat, her face hidden by a hood, she walks out at night, without a guard or even a handmaiden to follow her, a long, sharp dagger concealed beneath her clothes.

She finds what she is looking for: silent resentment, sleeping revolt; and hands that deal out poison for gold and ask and answer no questions. It is not long before she also finds magic: she dives at it with a desperate fury, unrepentant.

xxx

Terrible premonitions haunt her dreams. She wakes up screaming, Gwen by her bedside with tears of fear in her eyes, until she can no longer bear it and sends her away. Then she wakes up alone: a few times, she thinks of telling, of warning Uther, against all reason, before she remembers.

She starts hating him again, for having loved him.

xxx

She is caught, of course, with poison in her hands and magic in her pockets, and sealed lips. She stares down the guards that come to her as she always has, swears to herself to suffer anything before betraying anyone.

All traces of magic disappear in passing from Arthur's hands to Uther's. She is confined to her rooms, a prisoner in her own home. The king refuses to see her. Gwen alone goes in and out, brings her news and flowers, and stares at her with kind and terrified eyes.

xxx

The reconciliation is slow and painful, and of course never complete. But she knows to lie as well as to be brutally honest, and Uther loves her more than he knows himself. Maybe only Gwen notices her smiles are strained and forced, and Gwen remains silent.

xxx

They find a poisoned dagger by Uther's bleeding corpse, and his locks opened by magic.

xxx

She's at the funeral but not the coronation and all the following fests, the guards by her door more silent and incorruptible than Uther's ever were, and even Gwen separated from her.

Arthur comes only several days later, head high under Uther's crown, Merlin in his trail, carrying a staff and wearing ridiculously extravagant robes – Arthur's doing, of course – and smiling a little helplessly at her, and she knows at once. Did Arthur know all this time, she wonders, a little hurt? It matters not: this open, showy acknowledgement is betrayal enough.

"You're a traitor as well," she says, before he can speak, pointedly looking at Merlin; her tone is challenging, but not disapproving: she is immensely glad Arthur would do this.

"Morgana," the king says, and looks at her for a long time, and like he's seeing her for the first time. Quietly, he adds: "I don't want to know. But you will leave Camelot tonight, and you will not return."

She's careful to avoid Gwen, or else her hearth would break.

xxx

She doesn't call them, but when they come, she doesn't close her door to them.

She can differentiate them: bandits and revolutionaries, idealists and cynics, people she knows from her days as a shadow creature in Camelot and new ones, even these who wish Uther's days back, and she can pick and chose.

Druids and magicians too, after a time: magic is no longer forbidden in King Arthur's realm, but still regarded with suspicion and carefully monitored, more efficiently than ever now that the king has Merlin – Emrys, they call him – by his side; the great dragon is still a prisoner under the castle, and yet the king has a magical sword forged in its breath at his side. And soon, nowhere in Albion is there any escape.

They teach her to use her own gifts, and to recognise her dreams for what they are; and they bring the druid-boy she once saved to her, with reverence: sometimes, forgetting he is but a child, she tell him all her bitter anger and disappointment. He listens, with his fix, attentive eyes.

xxx

Gaius comes, with a reprieve that allows her to return to Camelot, and messages of affection from Gwen, and suspicious glances to her entourage. She receives him well, but she thinks of his silences and his potions when she came to him with her frightening visions, and listens not.

xxx

An invitation follows the reprieve, to Arthur's marriage. She thinks, he cannot do that, how dare he do this to Gwen: he doesn't want her, he wants one of us, who went with him to save one village and knew him before he was a great, wise king to which knights of all realms come to swear allegiance, and he can't have me, and he can't have Merlin.

If Gwen was there, she might have said: "don't do this, you will be unhappy." If she could talk to Gwen, maybe she would have pressed her: "accept, you will be safe." If Gwen could still calm her with her embrace and she could forgot the horrified look in her eyes when they found her with the poisons, maybe she would have listened to her and told her: "all I want is for you to be happy; I will be there for you, no matter what."

But Gwen is far away and out of reach, and she writes angrily: "Refuse. Come. If you do this, I will consider you my enemy as well."

Later, she wonders when exactly Arthur has become such.

xxx

The response comes shortly thereafter, written in Gwen's own hand, pleading in its uneven pace:

I won't, if you come back.

I miss you. We all do.

I love you.

She watches the parchment burn for what feels like hours.

xxx

It is years later, that Lancelot falls into her hands by pure chance.

His prison is a gentle one. She installs him in her most luxurious chamber and serves him the best meals, and he suffers of nothing but boredom and inaction; she doesn't refuse him when he asks for material to paint to chase away these.

She wishes she had.

His pictures are simple but artful and unmistakable. Gwen, still a seamstress, preparing him for his meeting with the prince; Gwen, straight and regal and strangely unchanged, greeting the knight after his long-awaited return to Camelot; Gwen, walking by his side by a stream, without anyone following them, against all conventions; Gwen, letting him knee down before her, giving him her hand to kiss; Gwen, giving Lancelot a ring that Morgana recognises at his finger; Gwen...

Morgana sets him free before she can learn too much, with no conditions but that he wait at least a year before returning to Camelot.

xxx

When Arthur knocks at her door, seeking entrance, she's close to refusing him, but he's there with what looks like half an army, and he's king of Albion.

They talk very little, he needs only a shelter for the night. She has never seen any of the knights that are with him except in visions. Merlin is not with him; he, maybe, could have prevented this.

He stops dead, when he is lead to his chambers, and sees the decoration left there from Lancelot's captivity, while she tells him, falsely cheerful to hide her low-burning anger, who made them. And then, as he stares at the walls and the ceiling, a terrible look of betrayal passes over his face (whose, she wonders later: Gwen's, Lancelot's, even her own for showing him this?)

He leaves, without another word to anyone.

For many nights, the scene is replayed in her dreams and chases away the visions.

xxx

She calls Merlin, reaches him through the misty corridors of their art; he comes, but he too has changed: he looks at her with suspicion and coolness, ready to strike if need be; all her discourses, threats and pleas and remembrances, die on her lips. All she says is:

"You won't let him hurt Gwen."

He bows his head quietly.

"I won't let him hurt Gwen."

It's a promise.

xxxx

The bits about Lancelot are based on Arthurian legends retellings; I don't know which version(s) they're originally from myself.

Comments are much appreciated!