Set around the time of "Lancelot and Guinevere" but doesn't really pertain to any specific episode.
It was surprisingly easy to hide their relationship from Uther.
Part of it was that Uther only ever saw what he wanted to see, and if he didn't want to see his son in a homosexual relationship with his manservant then by God he wasn't going to see it.
At first they were extremely cautious. Merlin would pretend to go to sleep in his room, wait until Gaius had fallen asleep, and then sneak back into Arthur's room, slipping away at dawn to return to his own quarters. Arthur stopped touching Merlin in public at all, until Morgana asked him if he'd had a fight with Merlin and pointed out, with a bit of glee, that usually he couldn't seem to keep his hands off him. While Arthur had a few choice words to say about that, he had to admit that he had a habit of doing things like hauling Merlin around by his shirt collar, shoving him, thumping him on the shoulder, and the like.
They'd even refrained from hickeys, which was a lot harder to stick to when Arthur realized how addicted he was to Merlin's neck and collarbones and Merlin realized he rather liked biting Arthur's shoulder.
But as time went on and people didn't start whispering whenever they entered the room and the servants didn't start shunning Merlin and Morgana didn't trap Arthur in a corner to lecture him on taking advantage, as if Arthur could possibly make Merlin do anything he didn't want to do, they realized that they really didn't have to be so careful. So they relaxed a little.
Merlin promptly moved into Arthur's room (which meant Gaius had to be told, and that was a whole different story), Arthur endured Gwen's squeals because Merlin insisted she be told because she was his best friend or something ridiculous like that, and life went on as usual.
Which still left Uther.
While Gwen and Gaius seemed not only accepting but absurdly pleased with Arthur and Merlin's relationship—which baffled Merlin and greatly concerned Arthur—neither of them had any doubts as to what Uther would think about it. At best, he'd exile Merlin. At worst...
And then Gwen was captured by Hengist, Uther refused to rescue her, and Arthur got, well, pissed off. Servant or no, Gwen was a loyal woman, intelligent and loving, and had assisted both Merlin and Arthur more times than the prince cared to count. His father's callous behavior toward the lower classes—which included Merlin—made Arthur's blood boil.
Which led to an odd sort of rebellion in which Arthur fucked Merlin on the council table.
When Uther next held council, he wondered at the odd sticky texture, complained that someone hadn't cleaned up the wine properly from the banquet last night, and demanded a servant clean it up.
Merlin had flushed bright red and tried not to run out of the room from embarrassment.
Arthur just smirked.
It turned into a strange sort of game. Uther did something, Arthur grew angry, and he convinced Merlin to have sex somewhere pertaining to state matters. The council table saw a lot of action, as did the throne on two memorable occasions, plus the rug underneath Uther's dining table, a few pillars in the throne room, and directly underneath the Pendragon coat of arms.
It was shockingly easy to hide their relationship from Uther.
Sometimes, Merlin wondered if Arthur was even trying.