This whole post is full of spoilers for the latest season of Game of Thrones, so please turn away if you are the kind of person who is bothered by that.
Bran Stark's latest vision in Game of Thrones' season six finale "The Winds of Winter" finally reveals what superfans of George R.R. Martin's A Song of Ice and Fire have long suspected: Jon Snow is not Ned Stark’s bastard son at all. He’s Ned's nephew — the son of Ned's late sister Lyanna Stark, and of Rhaegar Targaryen, Daenerys’s older brother.
Clues to this effect have been sprinkled hither and yon throughout the vast backstory revealed in Martin's novels, and the theory — known as R+L=J — is sufficiently accepted in the fandom that the show’s revelations hardly count as spoilers. Nonetheless, there is a difference between a widely believed theory and a confirmed one, and the latter is what we now seem to have.
Within the fiction itself, meanwhile, this revelation significantly changes our understanding of several different aspects of the story. For one, it establishes Jon as a potentially legitimate claimant to the Iron Throne. It also establishes a Targaryen heritage for Jon, which may let him wield dragons or fire immunity in whatever action is to come in future episodes. But it also undermines Jon’s claims to leadership in the North, and most of all it undermines our Stark-centric view of the backstory to the entire series.
A short history of Robert’s Rebellion
As you may recall, when Game of Thrones begins, Robert Baratheon sits on the Iron Throne, assisted by his younger brothers Renly and Stannis on the Small Council. Jon Arryn, lord of the Vale, has served for years as hand of the king but is now dead, and King Robert is asking his old friend Ned Stark to take over for him while Viserys Targaryen lives in exile, dreaming of retaking a throne that is rightfully his.
This all comes about due to an epochal event known as Robert’s Rebellion.
The history of this rebellion has been taught to us by the winners, and it goes like this:
- Robert Baratheon and Ned Stark were living in the Aerie under the tutelage of Jon Arryn as fosters.
- Robert was engaged to marry Ned’s sister Lyanna.
- Rhaegar kidnapped Lyanna, and Rhaegar’s father — King Aerys II — had Ned’s father and his older brother killed when they complained about it.
- Aerys then demanded that Arryn hand Ned and Robert over to him. Arryn refused, and led Houses Arryn, Stark, and Baratheon in a successful rebellion that House Tully joined after both Ned and Jon were engaged to Hoster Tully’s daughters. House Lannister joined at the last minute.
- Robert took over as king because he was a distant Targaryen cousin, appointed his mentor Jon Arryn to serve as hand, and married Cersei Lannister to further cement the alliance.
At the end of the war, as previously seen, Ned and Howland Reed fight Ser Arthur Dayne outside the Tower of Joy to find Lyanna but she does not survive the war.
Ned then returns to Winterfell with a baby, Jon Snow, who he presented to the world as his bastard son and raised among his trueborn children. Ned never told Jon or anyone else who his mother was. What we see in this episode is that Lyanna was pregnant during the war and gave birth to a child — presumably Rhaegar’s son — shortly before dying. This is the baby that Ned brought back with him to Winterfell. Not his son, but his nephew.
Why would Ned lie about all this?
Well, way back in season one we see Ned and Robert — who are close friends and political allies, let's recall — arguing about whether they should assassinate Daenerys way off in distant Essos. Robert, you see, believes that any surviving Targaryen child is a mortal threat to his regime. Ned believes that murdering children is wrong and they should let Daenerys be.
Also recall that, as has been mentioned several times in Dorne-related plots, upon joining the rebels the Lannisters sacked King's Landing and immediately murdered the two Targaryen children they could find.
Ned and Lyanna would both know, in other words, that the new regime could never allow Rhaegar's son to survive. Ned, not wanting to murder his nephew, came up with the idea of simply pretending that he's not Rhaegar's son. He would, instead, claim Jon as his own son by some unknown woman and then raise him among his family up north.
But now, years later, Jon's Targaryen blood would seem to set him up for something to do with dragons and perhaps a bid to sit on the Iron Throne as part of his larger mission to save the human race.
What are the implications of R+L=J?
One set of implications relates to the politics of the North.
Here Sansa, by law, ought to be Ned’s heir now that all his sons are dead. But the fact that Jon is a man and has been widely known in the North for years as Ned Stark’s son, combined with the fact that he leads an army, has given him a strong de facto claim to political authority. If he’s actually Ned’s sister’s son, then his claim goes from questionable to garbage.
On the other hand, it turns out Jon might have a decent claim to the Iron Throne.
The son of Aerys’s son Rhaegar should have a legally superior claim to Rhaegar’s little sister Daenerys.
It’s true that Jon is, as far as we know, a bastard. But it’s also true that Targaryens practiced plural marriage, and for all we know Rhaegar and Lyanna were legally married — at least in Targaryen eyes.
And regardless of the legal details, if Jon has Targaryen blood in his veins that may mean he has Targaryen superpowers, including immunity to fire and the ability to ride dragons. That’s the sort of thing that could come in hand when fighting an army of ice monsters. Conveniently, there’s longstanding speculation that the hot springs that keep Winterfell inhabitable have something to do with a dragon or dragon’s eggs in the crypts beneath the castle.
If Ned’s story about Jon isn’t true, what else isn’t true?
That’s an excellent question.
Basically everyone in a position to know — Varys, Jamie, Doran Martell, etc. — agrees that Aerys II was a bad king, and the part of Robert’s Rebellion where he overreacts and makes everything worse by threatening to kill Robert and Ned makes sense.
But everyone who worked alongside Rhaegar seems to think he was an all-around good guy and remembers him well. Why would he kidnap the daughter of one of the most important lords of the realm, who happened to be betrothed to one of the other Great Lords of the realm and whose foster father was a third Great Lord? That’s awfully impulsive.
What if Lyanna ran off with Rhaegar out of true love, despite her betrothal to Robert? That would change the narrative somewhat. What's more, though arranged marriages are certainly par for the course among the Westerosi nobility, there's no good reason for the Starks to have preferred a match with Robert Baratheon to one with the heir apparent to the Iron Throne.
Unless, that is, the intertwined network of houses Baratheon, Arryn, Stark, and Tully that ultimately brought down the Targaryens was conspiring to overthrow the ruling house since before the alleged abduction. This is the "Southron Ambitions" theory, which is much broader and less specifically grounded in the text than the core R+L=J theory.
According to Southron Ambitions, Mad King Aerys was much less paranoid (though no less brutal) than his "official" portrayal, and was combating a very genuine threat to his rule that existed long before the specific Lyanna crisis. At a minimum, Southron Ambitions posits a "just because you're paranoid doesn't mean they're not after you" view of Aerys's downfall.