Okay here it is, not sure if others thought of this but I am well chuffed. Spoiler tags for good reason, only read if you have read all the books thus far or don't give a hoot.
Jon Snow is not Ned's bastard, he is the child of Lyanna and Rhaegar Targaryen. The three remaining Kingsguard are guarding her when Ned finds them in the Tower of Joy after Rhaegar supposedly "abducted" Lyanna, like some people think he was a villiain and abducted her (Robert) some think Rhaegar was a decent person (Barristan). Most seem to agree he was a decent and honorable person and that people use his mad Father as a cop out to explain what happened, like he was mad too. However, it seems to be more likely that he was in love with her after crowning her the Queen of Love and Beauty after the tourney at Harrenhal.
When Ned, Jory's dad, some others and Howland Reed face Arthur Dayne and the other kinsguard the kingsquard are slain, then finds Lyanna lying in blood. You don't know what happens next, Lyanna dies in a pool of blood and a promise is uttered to which you never know the full extent of (only that she wanted to be buried in Winterfell).
Ned returns home with a child claiming it to be his bastard, though never speaks of the mother.
I think Lyanna died in childbirth to Jon Snow, The Kingsquard were protecting him and Lyanna as their last duty to the rightful king since Rhaegar and Aerys were dead, knowing what would befall him should the truth come out, Ned adopts him as his bastard son.
The only person alive who knows the truth is the Crannogman Howland Reed who never appears or speaks about it, but I think it will be revealed at a later date.
What do you think?