(Warning! This post contains spoilers from all of Game of Thrones' sixth season, including the episode 10 finale "The Winds of Winter.")
The question of Jon Snow's parentage has been a persisting mystery since the very beginning of the series. Years ago, fans of George R.R. Martin’s A Song and Ice and Fire series began speculating that the question wasn’t simply in regards to Jon's mother, but his father’s identity as well.
Tonight, on the Season 6 finale, the show confirmed the long-running and widely accepted fan theory referred to as R+L = J, or Rhaegar plus Lyanna equals Jon.
Bran and the audience returned to the Tower of Joy, last glimpsed earlier in the season, where we saw a young Ned reach his sister, Lyanna, just before she died in childbirth. Lyanna whispers something to Ned, and says: “If Robert finds out, he’ll kill him. You know he will.”
Ned is handed a newborn and promises to protect his sister’s child. The shot immediately cuts from the infant’s face to present day Jon Snow, confirming that he’s not Ned’s Stark’s bastard son after all; he’s his bastard nephew.
So here’s everything you need to know about Jon Snow's backstory:
Rhaegar Targaryen was the Mad King’s eldest son and heir, and the older brother of Daenerys and Viserys. Dany was born after Rhaegar was killed in battle. Robert Baratheon's Rebellion was instigated by the disappearance of Lyanna Stark, who was allegedly kidnapped by Rhaegar.
Rhaegar was already married and had two children with Elia Martell, Oberyn Martell’s sister, the one he was trying to avenge against the Mountain in Season 4. Lyanna, meanwhile, was promised to Robert, who loved her desperately. The truth of her disappearance is not known— while the commonly-accepted story was that Rhaegar kidnapped and raped Lyanna, some fans speculate that she could have willingly chosen to go with him.
When Lyanna’s father and eldest brother rode to King’s Landing to demand Lyanna’s return, the Mad King had them killed, spurring the Baratheons, Starks, and Arryns to overthrow the Targaryen regime.
The war lasted nearly a year, giving Lyanna enough time to experience a full-term pregnancy. Robert killed Rhaegar at the Trident, Jaime Lannister stabbed the Mad King in the back, and Ned tracked Lyanna down to the Tower of Joy. Earlier in the season, we saw him face off against Rhaegar’s men, who we now know were guarding Rhaegar's child and Lyanna.
After the events inside the Tower, Ned raises Jon as his bastard, keeping the secret from even his own wife, as Jon’s history put him in immense danger. Not only would a living Targaryen heir pose a threat to Robert’s claim to the throne, but he was a jealous, violent man who would never have allowed Jon to live, believing him to have been the product of the rape of his betrothed.
So Jon is a Stark, he’s just not Ned’s son. The kids he grew up believing to be his half-siblings are, in fact, his cousins. And Daenerys is his aunt.
Does this mean Jon’s going to sit on the Iron Throne? He is still a bastard, so he doesn’t have a legal claim to the Iron Throne (or Winterfell, for that matter, though he was proclaimed King in the North anyway). Besides that, the throne currently belongs to the Baratheon line, so Jon’s Targaryen blood would not give him access. With the Baratheons and their heirs (or in the case of Cercei’s children, “heirs,”) all dead, it’s unclear who is legally next in line, though Cersei simply circumvents the rules and claims it for herself.
Were the Targaryens to be restored and Jon to be legitimized, he would technically come before Daenyres in the laws of succession. As Rhaegar was the Mad King’s heir, any offspring of his would supersede additional children of his father’s, including Dany.
He was already declared King in the North (against all odds), so there’s no telling where the show may take Jon. Although, as we know, greater wars are coming and the game of thrones isn’t so important in the face of an undead army descending on the Seven Kingdoms. There may not be an Iron Throne to sit on by the end of it all.
This reveal also puts Jon at the top of the list of potential dragon riders. Dany has three dragons, but so far is the only human who can ride them. Now that there's one more Targaryen in the world, there's a chance Jon may hop on a dragon and roast some White Walkers.
First things first: Bran has to deliver this new information so that the rest of the characters know what the audience now does.