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.
A vision experienced by Bran Stark in his mystery cave brings Game of Thrones to the edge of revealing something readers of the books have long believed but have been unable to prove: Jon Snow, everyone's favorite no-longer-dead bastard Lord Commander of the Night's Watch, is not Ned Stark's bastard son at all — he's his nephew (and also Daenerys's nephew), the product of a union between Rhaegar Targaryen and Ned's sister Lyanna Stark.
Clues to this effect have been sprinkled hither and yon throughout the vast backstory revealed in George R.R. Martin's novels, but the sparser storytelling constraints of television have in some ways made it clearer. The show has no space to waste on irrelevant backstory, and the fact that the creators have bothered to show us Ned fighting his way into the Tower of Joy to find Lyanna is a drop-dead clue that there's something important happening there.
The full upshot of this reveal will, of course, unfold over time. But the inclusion of the scene will bolster the longstanding fan theory, and a Targaryen heritage for Jon is significant on a number of levels.
For starters, it means he has a plausible claim to the Iron Throne — not just to Winterfell — a claim that would be strengthened by marriage to Daenerys, which would be a convenient way of bringing together the two main surviving "good guy" protagonists of the series.
Additionally, the books have extensively set up a prophecy believed by followers of the Lord of Light — that a promised hero, Azor Ahai, would return and save the world from darkness. Melisandre thought that hero was Stannis — but in one chapter she searches for him while staring into her magical flames, and says, "All I see is Snow" — with a capital S. If Jon's father is, in fact, Rhaegar Targaryen, that would mean Jon is the blood of the dragon as well as a Stark — a fitting lineage for a mystical hero in a series called A Song of Ice and Fire.
Wait, who are all these people again?
Most of the key players in this drama have been dead for years, sometimes dating back to well before the beginning of the series, so most viewers would benefit from a refresher:
- Ned Stark: At the beginning of the show he is Lord of Winterfell and Warden of the North. He is appointed Hand of the King by Robert Baratheon and, after King Robert's death, deposed from office by Cersei Lannister and executed at the behest of her son, the new king, Joffrey. As depicted in this week's vision sequence, before the events of the series he was a key ally and supporter of Robert during a rebellion against the Targaryen dynasty led by the Houses Stark, Baratheon, and Arryn.
- Robert Baratheon: The king of Westeros at the beginning of the series, he seized power before the show began by leading a rebellion against the Targaryen dynasty, whose last scion was the "Mad King" Aerys Targaryen. Robert and Ned were raised together as foster brothers in the household of Jon Arryn, who later served as Robert's Hand of the King and whose murder sets off the events of the series.
- Lyanna Stark: Ned's sister, who never appeared in the series. She was betrothed to Robert before the rebellion against the Targaryens, and years later, at the opening of the show, Robert still speaks of his love for her. The precipitating event of the rebellion was Lyanna's kidnapping by (or perhaps elopement with) Rhaegar Targaryen. The then-heads of Houses Stark and Baratheon tried to get her back and were killed by the "Mad King" Aerys Targaryen for their troubles, and then Robert, Ned, and Jon Arryn rebelled against his rule.
- Rhaegar Targaryen: Rhaegar was Aerys's eldest son and heir. Unlike the Mad King, Rhaegar was generally well-liked and well-respected by those who knew him, which makes his decision to run off with Lyanna a bit puzzling. During Robert's Rebellion, Rhaegar left Lyanna behind at the Tower of Joy under the watch of the Kingsguard while he went off to the front to combat the rebels.
What's the significance of what we saw?
Ned Stark, along with several leading northern companions, is depicted fighting his way into the Tower of Joy past a number of members of the Kingsguard including the great knight Ser Arthur Dayne. Their goal is to rescue Ned's sister Lyanna, who, somewhat puzzlingly, is being held by the Kingsguard even though this has prevented Dayne from fighting in the decisive battle of the war.
Superficially, we are simply getting some backstory here about Ned.
But there is something very odd about all of this. The war, at this point, is already over. By the time Ned journeys down to the Tower of Joy, he and Robert have already defeated the main Targaryen loyalist army. Tywin Lannister has already switched sides and helped sack King's Landing. Jaime Lannister, a key member of King Aerys's Kingsguard, has already killed him.
Dayne et al., in other words, have nothing left to fight for. And sending several high-profile knights to guard a single woman in a remote tower seems bizarre anyway.
What could possibly be so valuable? The answer is the baby — Rhaegar's son, a potential heir to the Iron Throne and thus a threat to Robert's legitimacy.
What does this have to do with Jon Snow?
The theory — R+L=J — is that Lyanna is in the tower because she was pregnant with Rhaegar's baby, and that baby grew up to be Jon Snow.
Ned found him, claimed him as his own bastard, and then took him back north to raise him far away from the politics of King's Landing.
Why would he do that?
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 broader implications of R+L=J?
Contemplating the R+L=J scenario is also a reminder that the vast majority of what we know — or "know" — about the recent history of Westeros amounts to history as written by the victors. The Starks, the Lannisters, and Renly and Stannis Baratheon all ultimately fought against the Targaryen dynasty. Daenerys was too young to have any recollection of the relevant events. House Tyrell fought on the Targaryen side of the war, but we haven't really heard their perspective on its outbreak.
In the victors' telling, the realm was beset not just by the Mad King but by a sudden and entirely irrational action on the part of his previously not-mad son, who for no reason at all kidnapped the daughter of one of the most prominent nobles in the land while she was betrothed to one of the other most prominent nobles.
But what if this is wrong?
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.