Been thinking about what Mordred's life in Camelot would've been like if Merlin didn't hate him and then thought about how if Morgana was around she would probably always give him her favor at every tournament (until he married) and the other knights would tease him for that so have a broad outline for a Beloved Characters Dont Turn Evil AU
Morgana discovers her magic and Merlin swears to her that he'll protect her. He comforts her when she's scared and Merlin begs Gaius to share his knowledge and suspicions about Morgana to Morgana herself. One night Morgana bursts into their quarters in hysterics, waking them up, screaming and sobbing, and it feels like Merlin's hug is the only thing holding her together but its not enough. Glass starts shattering, candles flare, chandeliers fall to the ground. Gaius decides at this point not telling her will do considerable more harm than not, to both herself and others. They stay up through the night. Gaius speaking and Morgana asking questions, Merlin with a supportive hand on Morgana's shoulder. At one point Morgana tearfully asks the question Merlin asked Gaius long ago, "am i a monster?". They all fall asleep at the table, and that morning when Gwen arrives to wake Morgana only to find her absent with her blankets thrown over the bed and several things knocked over she runs and alerts the guards. The guards initiate lockdown and the commotion reaches Uther and wakes Arthur (Merlin is once again late), and they proceed to fear she was kidnapped right under their noses without anyone knowing. Arthur runs down to get Merlin so he can prepare him for the day only to open the door to find the three of them asleep on the table.
Later Merlin organizes for Morgana to learn more than Gaius can tell her from the Druids, but she intends to stay the night at least, if not then significantly longer (anywhere from a week to several months), and they have no good excuse for her to use that would allow her to leave without Gwen and guards. They come up with some very convoluted plan, which does not end up in the raid that occurred in canon, and when Gwen catches her sneaking back she lies and says she wanted to check up on Mordred (who she did run into), to see if he was with the Druid encampment that was rumored to be nearby (which he was). She didn't learn nearly as much as she hoped in those few hours, but they at least pointed her in a direction.
Morgause comes to town, and leaves Morgana her bracelet. After discovering it stops her visions Morgana takes it to Gaius, who reveals it was enchanted and looks similar to the one Lady Vivienne used to wear. Morgana states Morgause got it from her mother, but that Lady Vivienne was Morgana's mother and wonders how the bracelet ever got to Morgause. Gaius says there was a rumor that Lady Vivienne had a baby that displayed a affinity for magic, but Gorlois told Uther their baby had died before they even named her. Gaius reveals that the baby was smuggled out of Camelot and given to the High Priestesses, and Morgause might very well be that baby. Morgana begins to long for a connection with Morgause, to meet the sister she never knew of and recover something of her dead parents. When she begins secretly meeting Morgause, she tells Merlin and then asks him to come with her when she begins receiving lessons from her. Morgause tries to convince them that killing Uther is the right thing to do, but Merlin keeps reassuring Morgana that all they need to do is convince Arthur to change the law for when he is king, and he's not ready to do that now so theres no use in killing Uther before he's ready, and that she does love Uther and Uther does love her and would try to "fix" her well before he ordered her death. Morgause still wants him dead, to rush the prophecy of magic's return. Them sneaking out every few nights cements the idea that Morgana and Merlin are secretly dating in castle gossip.
Im not sure what happens with Morgause, but i think she would still take Camelot at some point and she would spare Morgana and by extension Merlin. Morgana and Merlin make sure to get Arthur out (and Merlin probably goes with him) because they dont trust Morgause to not kill him. Morgause reveals her heritage (and makes Morgana a Princess and her Heir) despite claiming the throne for people of magic and not the House of Gorlois, and the knowledge that Vivienne and one of her daughters were sorceresses leads Uther to believe he can not save Morgana from magic that is likely in her blood and THAT is what breaks his mental state. Morgana's real heritage is revealed soon after, with Uther informing Gaius that Morgana being a Princess is actually within her birth rights. Morgause continues Morgana's training because at some point Morgana has to become a High Priestess because canon. That or Morgause switches sides (this is a Beloved Characters Dont Go Evil AU might as well make it No Beloved Characters Are Evil AU) and she trains Morgana later after Arthur is a established King.
Morgause is overthrown and the Round Table formed. Arthur as well as several people in the castle know of or suspect Morgana of being a sorceress but he refuses to banish her, first believing it to have been out of her control (forced by Morgause) and later learning that her nightmares had been magic all along (how could he punish her for something he knows she had tried to get rid of for over a decade?). Perhaps he lets her keep the title of Princess, having always seen her as a sister (and someone who is compassionate for the people in a way royalty should be) and armed with the new knowledge of her being his actual sister. Everyone expects Regent Arthur to crack down on magic, its what Uther would have done and what the people want, so he does. Morgana becomes a advocate for magic, as she had been for Arthur in private as a Prince, and it scares people in the castle. They believe her to be working with Morgause, despite her arguments being for individuals' wellbeing and how punishments fuels hatred for Camelot. Several attempts are made on her life, many stopped by Merlin and Gwen and sometimes Lancelot. Arthur often "asks" Merlin for his opinion on magic and with Morgana's voice being public he feels okay with being straight with Arthur on what he thinks. Uther dies same as he did in canon: protecting Arthur from a assassination.
Mordred becomes a Knight because canon. Morgana is ecstatic to see him again and acts like a mother who hasn't seen her child in ages when she first sees him. Merlin has learned you often make the enemies that are destined to kill you (ex. trying to stop Morgana's visions from coming true) so he ignores Kilgharrah and doesn't hate Mordred (he is always wary though). Mordred alternates between childlike eagerness around the knights and following Merlin around while hero worshiping him (no one can figure out why. Their best guess is that Morgana is a mutual friend). In the beginning he kept messing up his name (calling him "Merlin" is just weird) and they often talk in their heads and therefore just stare at each other which has led to two conflicting rumors: theyre in love or they hate each other. Morgana often invites him to dinner, and when they dine with Arthur they easily slip into mind-talking (because chewing) and Arthur is convinced that they're making fun of him every time they do it. He protects Arthur when Merlin can't, often runs off to do side quests Merlin needs to do but cant get away to do, and often tags along with Merlin on his quests. Being able to share the knowledge of his destiny since Lancelot died (if he dies in this AU) relaxes Merlin's caution and allows him to be emotionally closer to him. Mordred enjoys being around Merlin and Morgana not just because he's Emrys and she's Morgana, but because they are the closest thing to home he has: they know what he is, they understand (bits) of his culture and make it possible for Mordred to share it with them, their individual magic sings strong enough to remind him of when he lived surrounded by it. He quickly grows to love them so very much and no one understands WHY. The knights tease him about it, and Morgana forcing Arthur to take Mordred on certain missions he isnt qualified for "so he can learn" does not help. Gwaine and Percival were planning to convince him that he couldnt compete in a tournament without a lady's favor because he's the rookie and his panicked look greatly amuses them only to find Morgana giving him her's before kissing his cheek. They were relentless after that, alternating between "lady's favors dont count if they're from your mom," "Mordred has a girlfriend," and whatever the medieval version of affectionately calling him "Bambi" is. Morgana sits in the stand's throne (since Arthur is competing) or besides it if Gwen is queen, and she flashes a smile at him when he comes out (Gwen too. He's a sweet kid with a baby face, of course he's one of her favorites. He also reminds her of Merlin when she first met him: kind, awkward, cute). This settles Mordred's nerves but has the unfortunate side effect of increased teasing. Merlin doesn't let it go to far, he never does, and gives them a distraction before running back to Arthur.
And then magic is brought back to the land and Morgana continues the work of the High Priestesses and helps the rebuilding efforts and they're still adventures and problems, but everyone Lives Happily Ever After