"To the High Priestess. Nimueh raised her?" Then why hadn't he seen her before then, and why didn't Morgause know who he was? Not that he was complaining, stopping her would've been harder if she knew him. It also might explain why she wanted attack Arthur, Uther, and Camelot - and maybe why she never sought out Morgana before. She hadn't come until after Nimueh had died. Why hadn't Gaius ever said anything though, since obviously he'd known if it'd been in that show.
His eyes went wide slightly when she said she knew, but it only took a second to realize she hadn't actually meant it like that. Morgana continued and while he didn't exactly understand, he tried to. He thought of the connection she seemed to have to Mordred as well, and if it was anything like the feeling she'd had for Morgause. Which was a little worrying because what the dragon had said about Mordred and Morgana, and what Morgause had already done. As much as he cared about her, she seemed to have an affinity with people who he would have to stop.
"I don't - It's great that you have family, a sister, but If it comes to it...Nimueh would've killed Arthur and Uther, Morgause has tried the same. I hate to ask, but --" He couldn't. She was beginning to forgive him, and as long as they were here it wasn't an issue. Merlin didn't want to think about what Morgana would do if made to choose between Arthur and her actual sister, especially since when he'd poisoned her it seemed she'd already been given that kind of choice before.