I'm a total n00b to this theory- I thought it was too far-fetched at first, but after I read all these clues I'm starting to believe it must be true!
This has probably been written tons of times before (I confess, I didn't read also all the other 23 threads) but I have some thoughts:
-In ASOIAF a couple of times there are people who look a lot like their uncle/aunts. There is Arya who looks like Lyanna, but also Gendry, whom Brienne mistakes for Renly. Could this be a hint?
-Ned feels extremely guilty about whatever promise he had made to Lyanna. If the promise is that he should keep Jon safe and hidden, why does he feel so guilty all the time? I mean, he did it.
Jon is safe and sound at the Wall (well, as safe as someone who's fighting wildlings and zombies in a hostile climate can be) and nobody suspects he's a Targaryen.
Could it be that Lyanna asked him to promise him something else, and he didn't keep this promise?
If she was in love with Rhaegar, she could have asked him to betray Robert and pass to Rhaegar's side, eventually win over the rebels so that Jon could live as a prince and maybe one day have a claim over the iron throne.
But Ned didn't do this, so that could be the reason why he feels so guilty towards Lyanna's memory and why he sees her crying blood and stuff.
-There's one thing I don't understand: how can Jon be legitimate?
He was born as the result of an affair between a married man and a bethroted woman, and Elia was still alive.
I read about the poligamy theory because the Targs used to do it, but it sounds a bit far-fetched since it doesn't seem to be a possibility in Westeros (nobody else mentions it as a possibility in "modern" era -except creepy Craster, but he's beyond the Wall anyway) and I can't see a Stark happily agree to share her husband/lover with his legitimate wife.
I believe that Rhaegar's intention was to legitimize Jon (hence the presence of the KG) but he didn't have the time to do it (he wasn't there when Jon was born and right after Ned made him disappear). I wonder if he did even know that his son had survived the birth.... so technically Jon would be still a bastard.
The King coult legitimize it so... assuming that Dany will eventually win the throne, I can't really see her saying "oh right, he's the rightful heir since male descendants come before females. Here, let me legitimize you and give you this iron throne..."
I've probably written things that have already been discussed over and over, so forgive me!
Edited by Natalie_S, 09 May 2012 - 09:24 AM.