I’ve rambled before (at great length) about how I feel about this scene and what it says about Merlin and Gwaine as characters, both together and separate from each other, but I just. I have so many feelings about this.
I’ve got feelings from both sides of things (and it’s all got this backstory with regards to their relationship post S3); here’s from Merlin’s side:
Gaius’ guilt hinges solely on the use of magic, and that is what makes Arthur believe Agravaine. Magic is condemnation enough; Arthur doesn’t need more reason than that, particularly after what happened with his father. And if we believe Merlin (which we’re meant to, since we don’t see it outside this scene), everyone is right there with Arthur. It’s regrettable, but he is clearly a traitor, and therefore deserves no sympathy, no concern.
Which doesn’t bode well for Merlin, for obvious reasons, and because of how close he and Gaius are — their relationship is enough to potentially cast suspicion on Merlin. Not that he hasn’t been in trouble for sorcery before, but things are different now.
Gwaine sitting there, for who knows how long, waiting for Merlin, only to have some throwaway comment about boredom and checking in on how Merlin was doing, that seems like a mockery. And Gwaine — well, they are friends, though not as close as they used to be, because Gwaine is a knight, and there is an imbalance of power between them now.
Furthermore, knights uphold the law of Camelot, meaning Arthur; even if they were friends before, Gwaine’s duty to Arthur supersedes any relationship he has with Merlin. It’s the knights who tend to bring in magic users for sentencing (and therefore execution). Lancelot was different, because he knew about Merlin beforehand, had supported and helped him. Gwaine, though, is unknown.
So Merlin is suspicious. And then with Gwaine’s throwaway comment about being bored and seeing how Merlin is? You can see it in Merlin’s face: how does Gwaine think Merlin is doing? It’s not some joke, or some game, or something to take Gwaine’s mind off of being bored. Gwaine can find his amusement elsewhere.
It takes some persistence on Gwaine’s part to get Merlin to see past Gwaine’s tendency to make light of situations when it isn’t appropriate and realize that Gwaine does care, and does believe him, and actually does want to help (and that’s roughly when he starts getting hearts in his eyes again for Gwaine).
And from Gwaine’s side:
The idea of being a knight that Gwaine had carried in his mind, going off of the stories he heard about his father, doesn’t exactly mesh with what he experiences. It had sounded like all go, all the time, never resting and always off on an adventure, helping those in need and fighting in mighty battles. Even though he grew more jaded as he got older, and grew to have a healthy dislike for kings and all that the nobility stood for, he still held with him the childhood glamour of what knights could do.
He didn’t expect the amount of time they spend practically sitting around, just waiting for something to happen to them, the time they spend training in patterned drills instead of refining their techniques in actual fights, or the amount of time he still has to waste away in a tavern. He has a cause, and he has a duty and a purpose and a connection to his father and those are all good things, but even though they train every day he still feels like he might be getting soft, getting slow and predictable. He’d expected something more.
He hadn’t expected Merlin to not really be friends with him anymore. The way it had seemed before, the way Merlin had been so keen on Gwaine becoming a knight, he thought they would still be close, that he could still talk to someone who understood him, but Merlin grew distant. Or maybe it was Gwaine who got caught up in his new position, the position he had earned rather than been entitled to, and who found himself with a whole mess of people he could consider friends, instead of just the one. Got so caught up that he forgot about that one friend.
So maybe he is bored, just a little, but Merlin has never really been a joke to him, for all that he has played pranks with the other knights, and Gwaine isn’t blind. He can see plainly that Gaius is more to Merlin than just a mentor, and he had seen how Merlin felt just talking about losing his father, before. It’s too unfair for a person to have to go through that even once. He doesn’t intend for Merlin to have to go through it again.
It doesn’t surprise him that Merlin doesn’t trust him, because why should he? After all, Gwaine has not gone to great lengths to maintain the friendship he’d declared between them. All he can do is stay and hope Merlin will let him back in.
(And then Merlin does, and then they hold hands underneath the table, and everything starts getting better.)