Something that I have been thinking about...Warning: Spoiler! (Click to show)
Don't know is this was spoken about or not but I think that Jon is the son of Ned's sister, Lyanna Stark. Lyanna was kidnapped by Rhaegar Targaryen, well what if Lyanna and Rhaegar had a son in between the time that she was kidnapped and Robert's Rebellion. They said that she died in Ned's hands when they went to save her, what if she asked him to promise to say that Jon was his son so that they wouldn't kill him.
Edited by MrSneakerman - 5/6/14 at 11:19am
Think about it. Everyone says that Ned is the most honorable man, even his enemies. Ned wouldst lie to save his life, why would he ever cheat on Catelyn? Ned didn't even tell Robert Baratheon who Jon's mom was and they were best friends, your best friends usually know who you smashing.
So if this is the case, then Jon is half Targaryen and half Stark. Also making him Dany's nephew. Would all this make him the true heir to the throne?