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Spoiler: Up to 2.07The Witchfinder
Morgana, Uther declares sometimes, longing and regret in his voice, is just like her father. Gaius never comments on this, but in his opinion Morgana is nothing like Gorlois. If Morgana resembles anyone, it is Uther himself, far more than Arthur does. She has Uther's way of dividing the world in friends and foes, in quickly taking offense, rarely, if ever, forgiving. Like Uther, she burns with the certainty of her own convictions, and like him, she has no idea how to handle doubt. Gaius watches her going from challenging Uther at every opportunity to withdrawing deeply into herself as her nightmares take over her life, showing little interest in anything or anyone around her anymore, and is more sure than ever he made the right decision. Why not teach her, Merlin asks in the beginning, why not tell her the truth? Her situation is different from yours, Gaius replies, and what he doesn't add is that he knows this through bitter experience, the kind of experience which leads him to a cell where he awaits sunrise and death by burning in the certainty that his king will not save him.
There is a cynical saying the Romans brought with them, or maybe the traders from Gaul did: Put not your trust in princes. Gaius used to disregard it. When they were young, full of hope and plans, he put all his trust in Uther, and it was an easy gift to give, together with loyalty and affection. Uther was different then. Gaius has to believe this. But even Nimueh would have admitted it to be the truth, for she, too, was compelled to serve him, and she rarely served anyone but herself. Uther was never a gentle man, true, he always had his temper and was full of arguments while rarely listening to those of others, but he strove for greater justice and wanted to create something good beyond securing his own glory. The death of Ygraine drove him into grief first, and then into rage that burns to this day, fuelled by his own inability to ever look at himself and see the blame there, fuelled by the growing distrust and resentment around him. The bards compare kings to eagles in order to flatter them. Uther is a predator who has not flown anything but circles around his own pain for years.
Gaius remembers the first lies. When the Purge started, he believed Uther to be justified, to a degree. In the wrong hands, magic could do terrible damage, and there were more than their share of warlocks and witches who used their powers at the expense of others. As for the dragons, they were creatures of wonder and magic, and nobody in their right mind ever trusted them. They were never, ever, tame. That you could bargain with them if there was a dragonlord at hand was of little comfort to villagers who lost their homes and cattle because a dragon felt bored. This was that Gaius told himself when he gave Uther the first names. He would name the guilty ones, the ones who had harmed others, and Uther's grief and fury would burn themselves out through their punishment. He would come to his senses and return to ruling as the just, fair king Gaius believed him to be. Surely he would never harm anyone who did not abuse their magic. Surely. Then the first harmless village witch burned, and Gaius found himself sending anyone he cared for away from Camelot, proclaiming his ignorance to Uther, or downright lying about their supposed deaths. There were no more names from him, but he would never forget who had made those first arrests possible.
Merlin thinks there is a contradiction between Gaius taking him in and Gaius refusing to teach Morgana. Merlin is too young to see that both decisions spring from the same source, and naïve enough to believe the worst that can happen to you is losing someone you love to death. With any luck, he would never find out otherwise. The worst, Gaius thinks while Aredian interrogates him, the worst is watching that someone not die but becoming your own nightmare, and to know you have done your part to make this possible. But at least he will not have to do this twice. Merlin is his chance at atonement, because Merlin does not owe anything to the shadows of the past. He can be someone new. In more practical terms, he also listens, and he knows that he will not always get what he wants. Morgana, on the other hand, is the past made young again in front of Gaius' eyes. She spent her childhood and youth getting indulged, able to make people do whatever she wants, just as the young Uther has been. It's tempting, quite tempting to trust her. But Gaius knows in his bones what she'll do with this trust if it were ever given, because he has seen it before. Giving Morgana the truth about herself means giving her the truth about himself as well, and Merlin, and his one chance at redeeming the past. Would she be able to keep faith with all of this if, as it had done with Uther, something happened to turn her world upside down? No. She would sacrifice them to find her certainties again, Gaius is sure of it. Put not your trust in princes. Never again.
So Gaius makes his sleeping drugs for Morgana, changing the mixture each time in an attempt to find the one potion that will really allow her to sleep without dreams, for he has no wish to see her suffer. He is a loyal physician to Uther, and sometimes, as when Uther strides out to meet his death in place of his son and finds life instead, he feels that old mixture of pride and devotion, more fatal than any potion, flicker up in him again. He tries his best for Merlin, and tries not to think about the regret he feels when first waking up on the Island of the Blessed. It would have been a good and clean death, giving his life for Hunith and her son. It would have meant redemption. But life always is more difficult than that. It offers second chances, and it offers Aredian.
He'll burn Merlin and Morgana both if Gaius doesn't confess, Aredian says. Gaius tries to tell himself that Uther would never sacrifice Morgana, and that Arthur would save Merlin. But he does not really believe it. He can't anymore. Put not your trust in princes. Maybe that is why he survived Nimueh, though, why he has been kept alive through the decades when nearly everyone else who ever meant anything to him has died. He'll offer his life for Merlin and Morgana both, and the decisions he made about both of them will be justified because of this bargain.
After all, he has always tried to save them, to the best of his abilities.