I Have the Answer (Big Spoiler, Possibly)

[lucimay]

ok...so... who was secretly married to lyanna? who is the legitimate
heir to the iron throne? son of rhaegar or son of robert? (sorry its
all just a bit confusing to me)

i guess it'd have to be rhaegar right? cause robert never got the
chance to make a baby with her. so...was lyanna in love with
rhaegar rather than robert? Genly is robert's son, correct? we know
that due to ned's investigation. so...we've got jon snow, genly, dany,
and...eventually that last lannister kid possibly vying for the iron throne,
yes? i had always thought that eventually we'd see dany and jon teaming up against the threat from north of the wall but...will jon give up
the throne to stay at the wall? i believe bran will eventually be lord of
winterfell.

gah...i may need to re-read everything even as i watch events unfold on
the hbo series.

[I'm Murrin]

Jon Snow is the son of Rhaegar and Lyanna. The circumstances of how it all happened are unknown, but I think the things I point out in my post suggest that they were secretly married when he took her away to the Tower of Joy and got her pregnant, otherwise the child would be a bastard and have no legitimate claim to the throne, and hence wouldn't command the protection of the Kingsguard while more important things were happening in the realm.

Jon will stay on the Wall - as I mentioned, he gave up all his rights to inheritence and title when he swore his oath.

[Farm Ur-Ted]

So, did Rhaeger not have a sister? How come he was banging a Stark when he could have been nailing his sister (or maybe a cousin or his mom)?

[dANdeLION]

Jon Snow is the son of Rhaegar and Lyanna. The circumstances of how it all happened are unknown.

I'm pretty sure a few glasses of wine and a Barry White album were part of it......

[I'm Murrin]

So, did Rhaeger not have a sister? How come he was banging a Stark when he could have been nailing his sister (or maybe a cousin or his mom)?

Rhaegar's first sister was a young child, and his second was unborn. But he was promised to marry Cersei at the time, I think.

[I'm Murrin]

Arg, I've forgotten too much. Rhaegar was already married, to Elia Martell. The children Gregor murdered were his, not Aerys'. So it is very unlikely he was married again. So why did the Kingsguard defend Lyanna in her tower?

[SerScot]

Rhaegar was never promised to Cersei. Tywin simply hoped that Aerys II would allow Cersei to marry Rhaegar. Aerys was an ass who was jealous of the man who made the trains in his kingdom run on time. So, in a fit of pique, when Tywin offered Cersei as a wife for Rhaegar he told Tywin that his son would not marry the daughter of one of his servants.

That's why Tywin resigned the Handship and returned to Casterly Rock.

[caamora]

OMG! You guys are totally blowing my mind. I really need to re-read the series from the beginning. I've forgotten so many of these details.

I always knew that Jon Snow was the son of Lyanna but I could never figure out the father. I thought it might be Robert but then it wouldn't matter and Ned wouldn't bother trying to figure out who killed what's-his-face - the other hand so that obviously never worked.

Thank you because that was driving me crazy!

But you guys lost me with the Sansa not being a real Stark thingy. Please elaborate.

[caamora]

So, if Jon is a Targaryan, then perhaps we will see this come full circle and he and Danerys will marry and start a new dynasty.

[I'm Murrin]

Nah, as I pointed out, he swore his vows and he takes them seriously. He won't take Stannis' offer to release him and legitimise him, and he won't take any such offer from Daenerys.

One of the main themes of his storyline is that he belongs to the Night Watch now (it was the main point of his deserting to join the wildlings, for example - to reaffirm his place among the black brothers).

There's also the parallel of Maester Aemon, who was heir to the throne and instead took the black and forswore it all, and did not get involved even while his family were being destroyed. His telling Jon that story in the first book was a way of saying what lies ahead in Jon's own life.

[SerScot]

Murrin,

If the Wall is destroyed and the purpose of the NW ends, what then? That said I'll be shocked if there is a happy fairy tale Jon marries Dany founds new dynasty ending to ASOIAF.

[Zarathustra]

God, what a soap opera.

[I'm Murrin]

One of Arya's chapters in ASoS fills us in on the rest of the story, though of course it doesn't come out and say the actual truth.

Wylla, mentioned by Robert in AGoT, was Jon's wet nurse, and wet nurse to Edric Dayne of Starfall. His aunt was Ashara Dayne, thought of by Catelyn in AGoT as possibly Jon's mother, who had killed herself.

According to Edric (another Ned, Beric's squire), Ashara and Ned had met at Harrenhal and fallen in love, before Brandon Stark was murdered by Aerys.

If we piece together the story, then Ned killed Ashara's brother Ser Arthur Dayne at the Tower of Joy, found the dying Lyanna, retrieved her son Jon, and travelled to Starfall, where Jon was given to the wet nurse to care for while he had no one else. Ashara learns that her brother is dead at the hand of the man she loves, and that he has married Catelyn Stark, leading to her later suicide. Ned had already decided to keep Jon as his own bastard at the tower, where he swore Howland Reed to keep the secret, and so he also had a bastard child with another women when he turned up married at his lover's castle.

His honor, and the need to keep his promise to his sister against Robert's hatred of Targaryens, put Ned in quite the uncomfortable position.

[thranathiril]

One other thing that is another pointer to the R + L =J theory is one of the visions that Dany has in the Houses of the UNdying in Quarth. She sees a blue flower blooming in a wall of ice.

Blue flowers are mentioned in conjunction with Ned's memories of his sister. Jon is at The Wall.