So I've started rereading A GAME OF THRONES, and... it's like... hmmm... I never really noticed all these hints and portents before, but... is it possible that Jon Snow is Ned Stark's bastard child... by Ned's sister, Lyanna Stark? Is that the dreadful guilty secret he's lived with for the last fourteen years? Is that why Ned has never told anyone who Jon's mother is, why Ned won't even tolerate discussion of the subject? Most importantly, is it why Ned's response to learning that Cersei's kids were the product of incest was so bizarrely compassionate?
When you think about it, Ned's attempt to give Cersei a chance to run away with her and Jaime's kids is very strange. The typical response to children born of incest in Westeros is one of disgust and horror, and while Ned is certainly an unusually honorable man, and one could argue that he is even an unusually compassionate man, still, there's nothing in his character to indicate that his views on incest should significantly vary from his cultural norm... and certainly, there is nothing in his experience with Cersei and her children to cause him to want to save them, and, in fact, he has excellent reason to despise Cersei and, at the very least, Joffrey. Upon finding out that the kids are not Robert's, but are, in fact, the product of an incestuous union, why should Ned go out of his way to try to keep them from being killed by Robert's wrath?
Yeah, yeah... Ned has clearly been deeply troubled by the manner in which the youngest Targaryen children were slaughtered by the Lannisters, and so he grits his teeth and says "I don't kill children" to Cersei... but on the other hand, if Ned has no special reason to feel empathy for children born of incest, it seems like he might well feel that Tywin Lannister having to watch as Robert Baretheon murders his son and his daughter and his grandchildren is justice, or, at least, karma... and Ned is big on justice.
So, again... why is Ned so deeply moved that he goes out of his way to give Cersei -- a woman he despises -- a chance to take her kids and run, before he goes to the king, a man he loves as a brother, and tells him the truth about the parentage of Cersei's children?
The prevailing theory among fandom seems to be that Jon Snow is actually the son of Lyanna Stark and Rhaegar Targaeryen; that Lyanna and Rhaegar fell in love and ran off together, and that the general belief that Rhaegar kidnapped and raped her hundreds of times over a course of months is mistaken... and that keeping the truth secret, while pretending that Jon Snow is his own bastard child, is what Ned promised Lyanna he would do, as she died in his arms, presumably as a result of complications arising from childbirth. Yet Martin makes it clear over and over again that Ned still thinks about Lyanna, and his promise to her, every day and night of his life... that his promise, whatever it may have been, is somehow tied to some guilty secret that has wracked him with remorse every since. However, on page 381 of my copy of AGOT, Ned thinks a peculiar thing: "For the first time in years, he found himself remembering Rhaegar Targaryen. He wondered if Rhaegar had frequented brothels; somehow he thought not."
Now... if a day hasn't gone by in fourteen years that Ned hasn't been haunted by his promise to his sister Lyanna, and that promise has to do with concealing the fact that Jon Snow is Rhaegar Targaryen's son... how in the name of God are we supposed to accept that "for the first time in years, he found himself remembering Rhaegar Targaryen"?
If, on the other hand, Ned and Lyanna were lovers, well, it accords well with Ned's passionate devotion to Lyanna's memory, his absolutely unwillingness to even discuss Jon's parentage (even, or especially, with Robert Baratheon or his wife Catelyn), and his strange sympathy for Cersei's relationship with her brother and the children that relationship produced.
What prompted all this musing in the first place is a strange remark Tyrion Lannister makes to Jon the first time the two of them speak: "You have more of the north in you than your brothers." How can this be if Jon is half Targaryen? In fact, how can Jon have more of the north in him than his brothers... and in fact, Jon is frequently said to look much more Starkish than any of his siblings but Arya... unless both Jon's parents are actually of the north?