quote:
Theory:
Lyanna ran away with Rhaegar. Robert assumed she was kidnapped, and started the war to get her back. Rhaegar and Lyanna fled all they way to Dorne and holed up in the tower of Joy. When the Kingsguard went to find Rhaegar, they discovered that he had already left, so they stayed to protect Rhaegar's child by Lyanna. When Eddard & Co. showed up at the Tower of Joy and killed the Kingsguard, they found Lyanna with a baby. Knowing that the Baratheons and Lannisters had killed at the Targ kids, Lyanna made Eddard swear that the baby was hid ******* and not Rhaegar and Lyanna's child. Eddard never told Robert, who till the day of his death thought Lyanna loved him and had been kidnapped.
Now the only guy who knows about Jon's true parentage is Howland Reed. Incidentally, he's also the guy to whom Robb sent the document legitimizing Jon as the heir to Winterfell.
That seems the most popular theory, especially given how the books have played out. I can't remember if it was Feast or DanceWDragons, but other stories basically imply Lyanna and Rhag fell for each other. The story of the SheWolf and the tourney, plus Bariston's stories, etc.
All the evidence points to Jon being the "song of fire and ice" and really the only thing that goes against the theory is Martin seems to have made it so obvious in order to throw some crazy twist in it....
spoiler for those who haven't read DanceWDragons
well, that an that Jon very well may be dead after Dance