Morgana and Merlin have angry sex in her burrow. They start to meet up a lot, even though Morgana is still against the kingdom. At some point, Merlin chooses to check on Arthur over Morgana and he thinks she might be dead for a while. Morgana shows up with a bunch of priests(maybe?) and tells the court that she is with child from a sorcerer and that the child is prophetical by those priests' culture, or whatever. Gwaine finds out the child is Merlin's in the kitchen in the middle if the night, I think, and completely on accident when he says he knows how much Merlin loves Morgana, but Merlin thinks he's saying he knows the child is his and confesses that the child is his AND that he loves her. Gaius calls him an idiot, or whatever. Last chapter I read, I think, had Gwen asking if Morgana was in love with the father of her child.
I've been searching for this for a VERY long time and will sacrifice my best sheep for the person who can name this fic.