If the first things Peter said were meant to make everything better, to make it make sense, Claire was certain that she truly was in some kind of crazy world or insane dream. There was more to be angry at Nathan for in the telling, that he had known about the explosion. That meant that while she and Peter had been out trying to stop it, he'd known. That meant-
"He stood there, while we told him, and acted-" she whispered as he continued, but said no more. What was there to say? She'd known he couldn't be trusted.
But that anger was hard to hold on to when the blow came that he was dead, that Sylar had done it all and Nathan had been dead for years. Everything she'd blamed him for after the explosion, all the hostility about her life, what had happened to Peter, what had and did happen to all the others like them – and it hadn't been Nathan. Because he was dead.
How was it possible to feel pain about this when she hadn't even known him, when he was supposedly in this city somewhere right now? But it hurt, hurt more than she'd imagined it would have hurt to be told that kind of news, and she felt regret for what she'd just said about him... and this was all just too much right now. Rather than bolt, Claire clung to Peter again as the tears restarted, feeling crazy for mourning someone she hadn't really even known, but unable to do anything else.
Having retreated as far as he could without stepping off the roof, Nathan closed his eyes and pushed to keep the muting of the link in place on his end. He wasn't certain what Peter had told Claire, and even had he heard it he would have just agreed with what Peter had said about the wealth of reasons to hate him, but he could definitely hear Claire crying. He could only guess what had been explained but he felt certain it was an explanation of what had really happened in their timeline.
This was feeling too uncomfortably like eavesdropping now, however unintentional it might be. He couldn't go comfort her, and he certainly couldn't make this any easier for her short of staying right where he was, or so he assumed was the case. Perhaps hearing all of this was karmic punishment for his sins – a morose thought, but it was difficult to have light thoughts right now.