Ned isn't the only one who's upset, after what's happened. Robb and Arya are both inconsolable, and even Sansa is subdued, even though she takes her cue from Catelyn as regards Jon. Bran is too young to understand anything has happened, though to Cat's irritation he keeps asking for the boy. Still, whatever her feelings toward Jon, she isn't about to tell her little son that the half-brother he obviously cares for is ill to the point where Maester Luwin says that only the gods can decide now.
As for Cat... It damns her soul, and she knows it, but a part of her will be relieved if the boy dies. She knows it's not Jon Snow's fault that Ned sired him, not his fault that Ned brought him here to be raised with the trueborn children Cat gave him, but that doesn't make it any easier to be faced with him. She has too much resentment, and she decided long ago that her marriage needed to work, and to make that happen she could not resent Ned. So her bitterness falls to the boy instead.
But for now, Jon Snow lingers, and she goes to find Ned – he's in the godswood, praying for his son's life. Would he pray so hard for their children? He's always been protective of Jon, and she's wondered if he loves his bastard son more because he loved his mother more than her. Lady Ashara, or whoever the slut was. She pushes the thought from her mind, because she means to comfort Ned. He's grieving, and it's her duty as his wife to support him in such a time, even if she would rather the object of his pain have never existed at all.
She hates the godswood, and it only darkens her mood further, but she hears Ned before she sees him, or he sees her, and the words he is saying... It makes her stop in her tracks, eyes wide as she finally gets the answer to the question that has haunted her every time she looked at Jon Snow. But this answer is not what she would have expected, not even in the wildest theories she'd come up with.
“Please, don't take him. I know... I know I should not have lied about who he was, should not have said he was mine, but I had to! I promised Lyanna, I gave her my word that I would protect him. Please, if someone must pay for my lie, let it be me. Jon is all that remains of Lyanna, he's innocent, don't punish him for what I've done.”
Lyanna was his mother? And... Ned was not his father? That boy – he was a Targaryen-Stark bastard, conceived when Rhaegar forced himself on Lyanna? Catelyn didn't know if she wanted to laugh or cry, if she felt relief that the child was not Ned's, not the result of a love affair with a woman who meant more than she ever had, ever could, or if she was furious that he'd lied to her for all this time. That he'd brought shame on them and most of all that he hadn't trusted her. At first, perhaps, she could understand why he wouldn't; they were strangers then. But they hadn't been in a long time, how could he have...?
“Jon is Lyanna's?” It occurs to her that this is the first time she has called the boy by his name, but that's hardly important as she steps out by the hot springs, blue eyes dark with anger. Ned stumbles in his rush to stand and turn to face her, and he is obviously stunned to see her. But he reacts as stoically as ever, which only serves to frustrate her more.
“You heard me, then.”
“Yes, I heard you! How could you not tell me? How could you claim him as yours when he wasn't? Why did you not just tell the truth?” He could have; if the boy was a bastard he was no threat to the new reign, and if it came to it, he could lie about who fathered the boy in a different way – blame one of the dead Kingsguard if he had to. Why did he have to say Jon was his?
Ned is silent for a long moment, his grey eyes pleading with her to understand. “Cat, I couldn't. You weren't there – you didn't see...” He pauses, and takes a deep breath. It's obvious whatever he's about to say still haunts him, and some of Catelyn's anger fades at the sheer pain in his expression. “I was there, when Tywin Lannister's men brought Elia and Rhaegar's babes before Robert. They were wrapped in red cloaks – to hide the blood. They stabbed that little girl again and again – she was three years old, and they dragged her out from under the bed where she was hiding. And the boy, he was only a baby, not much younger than Bran is now. They dashed his head against the stone wall, Catelyn.”
He stopped, regaining his control, and then he said, “You know that, but you don't know that when Robert saw those bodies, he nodded in approval and called them dragonspawn. He may have loved Lyanna, but he would never have let her son live, not with Rhaegar as his father.”
Ned's words strike home, and for a moment she imagines Bran's head being slammed into a stone wall, or Robb's; she sees Arya and Sansa stabbed countless times. “But, why did you not claim it wasn't Rhaegar? Say one of the Kingsguard sired him?” It would have been a sensible lie, after all.
“They were honorable men, and no longer alive to defend themselves. I couldn't defame them that way. And in any case... Jon is not a child of force. We didn't know then, but Lyanna... She chose to run with Rhaegar, the kidnapping was a falsehood to hide the truth. They didn't know what would come of it.”
“So you defamed yourself?” But she isn't angry anymore, not really; her family's words are Family, Duty, Honor, but they could suit the Starks too. Family comes first for them, always; of course Ned had lied to protect his sister's son. Ned sighs.
“It was the only option left to me. The shame I face is nothing compared what I've condemned Jon to. I know it's been difficult for you to have him here – I know you must have thought his mother was a woman I loved, and you were right, but not in the way you thought. But he will have to live with the name I made him bear forever, and it will always count against him. I've done him a greater wrong than I did either of us, you must see that. But it was the only way to save his life, and now... It might not have even mattered.”
Cat thinks about that, and wishes she could argue. Because it has been horrible, having to see Jon and wonder where he came from, wonder who his mother was to Ned. It will be easier now that she knows – assuming Jon lives – but he will always be 'Snow' and always looked down on. He is a bastard and, she knows now, an orphan.
She steps forward and takes her husband's hand. “Let's wait and see if he recovers before you start thinking like that,” she tells him quietly. “You should come in; Robb and Arya are taking this badly, and I can't comfort them. They need you, and... Your nephew needs you too. You've done all you can for him, Ned.”
Later that night, when Jon's fever breaks and Maester Luwin says that he should make a full recovery, Cat still isn't sure how she feels. She doesn't know if she will treat Jon any differently now, even if she finds that looking at him is no longer painful. Her behavior towards him is habitual by now, and besides, if she becomes kinder to him, will it raise suspicion, risk undoing the story Ned told to save his nephew's life?
But as she told Ned, all there is to do for the moment was wait and see how things go. And, at least now she knows. That's a relief for her, and perhaps that relief, that ever-present question answered, will help her think clearly enough to know what to do next.