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The most popular fan theory in this series is R+L=J.  That Jon Snow's mother was Lyanna Stark and his father was Rhaegar Targaryen.  Meaning Jon is both ice and fire, and has the best claim to the throne (unless Young Griff is a real Targaryen, swapped during the sack on Kings Landing, in which case Young Griff has a stronger claim but most people discount that).

There is lots of evidence and very good basis to believe that

* Eddard Stark is not Jon's father
* Lyanna Stark is Jon's mother
* Lyanna Stark gave birth to Jon Snow in the tower of joy

What is less well supported is that Rhaegar Targaryen is the father.

The support includes:
1. Rhaegar 'abducted' or 'eloped with' Lyanna, so who else would be the father?
2. Three kingsguards were at the tower. It makes sense if they were protecting the heir to the throne
3. It develops the story very well if Jon Snow ends up being the rightful king.

But there is evidence against this, which has led me to continue to wonder about other options
1. Jon Snow has no Targaryen traits, has a double-helping of the North in him.
2. Jon Snow took the black, so he can't be King
3. Jon Snow was killed at the end of book 5 and the TV show is not canon. Jon may not come back, or if he does he would come back as a static character unable to learn and develop further (IMHO).
4. There is no evidence Rhaegar and Lyanna married, meaning he would still be a bastard and have no claim to the throne.
5. In contrast to the plethora of hints that Lyanna is his mother, there really are no hints that Rhaegar is the father. No dreams, internal dialogues of memories, symbolism, etc. No evidence of Jon being protected from fire (we have the opposite actually) or symbolism of dragons or the color red.  Nothing.

So... if you are still with me... who was Jon Snow's father?

I think this is the greatest unsolved mystery in ASOIAF and one that the greater fan base doesn't even recognize. 
 Any viable X+L=J theory will need to explain not only why the Kingsguard were at the Tower of Joy, but also why it was so important to Ned to protect the secret parentage of Jon Snow.

This is hard to do, which is why I think most people accept R+L=J and discount the fact that Jon doesn't have Targaryen traits.  They point to things like Baratheon hair being dominant in Cersei and Jaime's children, and so maybe Stark traits dominate Targaryen traits.

So it is a real challenge, and maybe it is a dead-end, but surely worth considering. 
 Hopefully Martin is reading this and the mystery will be revealed 
 Nice!
I remember reading (on the clock, procrastinating big time) these Jon theories back around 2010 on a wiki before the show existed 😉
I never came across the "well what if his father is a mystery?" angle... 
 
Yeah, if you go to the westeros.org wiki their defense of R+L=J https://awoiaf.westeros.org/index.php/Jon_Snow/Theories on this point is that many Targaryans don't have Valyrian traits.  However all those references are from outside of the book series (A World of Ice And Fire, Fire & Blood, The Rogue Prince, etc) which is not very satisfying.  GRRM should have put the evidence into ASOIAF itself.

I've watched a lot of AltShiftX and various other stuff, not sure I've seen Preston Jacobs. I'll go watch a few. 
 Wasnt Rhaenys Tararyan a black haired dragon rider in the books? Vaguely remember that somewhere. 
 Lilac eyes. Lean face. Dragon rider. Those are all Valyrian traits.  Jon Snow has none.

The much younger Rhaenys died in the sack on kings landing at 3.  She looked like a Martell.

There is enough evidence of Valeryan traits being recessive to keep alive the theory that maybe Jon Snow's father is Rhaegar.  I think GRRM might not even know - he seems to like to leave lots of things open ended. 
 He also retcons things.

I was referring to Rhaenys "the Queen who never was." Wife of Corlys Velaryon. Shes grey in the show but dark haired in Fire and Blood (though i think this was retconned from one of the essays). 
 Ok I just watched his whole series on the page of lies (9 videos, the last being hilarious).

I am convinced by it.  And I think you are right, I think blood will matter and parentage will not.

And given that Daenerys is of Dragonstone, not Targaryen, why shouldn't Jon Snow be of the North and also not Targaryen?

They both have the magic of their region in them.  And together they are ice and fire.

But neither of them is the rightful heir (if Jon's father is not Rhaegar, or if Young Griff is real)... that all these games of thrones are just the folly of man, blinding himself to what is real, what really matters (character, genetics), versus what is formally declared to matter (next in line to the throne based on dumb rules).

Thanks for the pointer, and I think this fits well with my preferred X+L=J theory. 
 Interesting points. Not sure we'll ever get our answers. Im holding onto a thread of hope that TWOW gets finished. No chance for a Dream of Spring. 
 Yeah me too, just a thread. 
 Wasnt Rhaenys Tararyan a black haired dragon rider in the books? Vaguely remember that somewhere. 
 Lilac eyes. Lean face. Dragon rider. Those are all Valyrian traits.  Jon Snow has none.

The much younger Rhaenys died in the sack on kings landing at 3.  She looked like a Martell.

There is enough evidence of Valeryan traits being recessive to keep alive the theory that maybe Jon Snow's father is Rhaegar.  I think GRRM might not even know - he seems to like to leave lots of things open ended. 
 He also retcons things.

I was referring to Rhaenys "the Queen who never was." Wife of Corlys Velaryon. Shes grey in the show but dark haired in Fire and Blood (though i think this was retconned from one of the essays). 
 Interesting points. Not sure we'll ever get our answers. Im holding onto a thread of hope that TWOW gets finished. No chance for a Dream of Spring. 
 Yeah me too, just a thread.